Plotting 23andMe markers density using karyoploteR

Learn how to plot 23andMe markers density on a karyogram.

Marcin Kierczak

25 minute read

Background

23andMe is a personal genomics and biotechnology company based in Mountain View, CA. It offers saliva-based direct to consumer genetic testing and it probably is one of the most popular choices among people who wish to learn more about their own genetic makeup, including genetic genealogy/ancestry analyses.

For genotyping, the company is using a technology known as DNA microarray, SNP array or SNP-chip. In short, SNP-chip is enabling us to “read” certain polymorphic sites in human DNA, the sites that are known to vary between individuals. Different versions of these polymorphic sites are, in turn, associated with several traits and features like eye color, blood group or a risk for developing certain disease. Now, it is not always the case that a certain version directly causes this or another phenotype. Often, a particular SNP is a good proxy for the phenotype, it tags the phenotype. This stems from the fact that we tend to inherit DNA in rather consecutive chunks (haplotypes or haploblocks) and often particular variant of a SNP is inherited with another variant in its neighborhood, the actual causative variant. Using this fact, one can save some money by genotyping only a limited number of SNPs to tell relatively much about many interesting traits. 23andMe is doing this. They have been using 3 different variants of their genotyping SNP-chip introduced in 2008, 2012 and 2014. I have been interested in visualising density of gentyped SNPs per fixed-length window along the genome to see how these 3 chips differ.

The data

23andMe uses Mendel Family as their showcase and we will look at the data generated for one of the members of the family – Lily Mendel (who happens to be a real person, Linda Avey, co-founder of the company). Data obtained with all three SNP-chips are available at SNPedia:

After unpacking the files, we see that the data format is rather simple – there are 4 columns describing each and every marker (SNP):

  • rsid – unique rs identifier of the marker,
  • chr – chromosome,
  • pos – coordinates of the marker,
  • gtype – the actual genotype, e.g. GG.

Analyses

Initial preparations

First, we have to load all the required packages and prepare our working environment. I have run itno some troubles with what turned out to be missing fonts. I have found a nice solution to this problem here.

#source("https://bioconductor.org/biocLite.R")
#biocLite("karyoploteR", )
library(extrafont)
# need only do this once!
# font_import(pattern="[A/a]rial", prompt=FALSE)

library("ggbio")
library("stringr")
library("karyoploteR")
library("biovizBase")

Loading the data

Now, we can load the data and fix column names. Next, we convert the data into GRanges object required for plotting marker densities.

gdata <- read.table(file = '~/Downloads/genome_Lilly_Mendel_v4.txt',
                    comment.char = '#')
names(gdata) <- c('rsid', 'chr', 'pos', 'gtype')

regions <- GRanges(seqnames = paste0('chr', gdata$chr), 
                   ranges = IRanges(start = gdata$pos, width = 2))

Plotting markers density

Finally, there is time to plot markers density on a karyogram. A karyogram is an ideogram showing ordered chromosomes, a map of chromosomes. We plot markers density over each chromosome using kpPlotDensity. What, I think, is a nice feature in karyoploteR is that on the karyogram it shows so-called G-bands. Giemsa staining is a specific chemical reaction that stains different parts of chromosomes in different way. It is widely used in cytogenetics to visualise chromosomes and their structure. There is one important parameter here – the window size which I have empirically set to 1Mbp.

kp <- plotKaryotype(cex=.7) %>% 
  kpAddBaseNumbers(cex=.5) %>%
  kpPlotDensity(data=regions, 
                window.size = 1e6, 
                col='slateblue', 
                border='slateblue')

So what?

Well, I think the visualisation is pretty neat, although we are missing Y axis… We will fix this soon. Apart from this, we can see low markers density around centromeres (central parts of chromosomes G-stained in red). We also see a long stretch of no marker coverage on the Y chromosome. Perhaps this is the non-pseudoautosomal region of the chromosome. Similarly, the density is very low at the beginning of chromosomes 13, 14, 15, 21 and 22 and we have an exceptionally high density on the short arm of chromosome 6. I have no idea why and not much time to research right now…

Plotting the actual marker counts.

Ok, so this was the density. What if we want the actual counts per window? Easy enough!

counts <- kp$latest.plot$computed.values$density
data_counts <- GRanges(kp$latest.plot$computed.values$windows, y=counts)
max_count <- floor(max(counts) + .1 * max(counts))

# Change the default plotting parameters
# Values established in trial-and-error
pp <- getDefaultPlotParams(plot.type=1)
pp$leftmargin <- 0.15 # Avoid chr names to overlap with the plot
pp$topmargin <- 150 # Avoid overlap between chromosomes
pp$bottommargin <- 150

# Do the actual plotting
kp <- plotKaryotype(cex=.7, plot.params=pp) %>% 
  kpAddBaseNumbers(cex=.5) %>% 
  kpLines(data = data_counts, ymin = 0, ymax=max_count) %>% 
  kpAxis(cex=.5, ymin=0, ymax=max_count)

As you can see, I did not manage to completely avoid overlap between chromosomes and their data panels. This can probably be further refined by playing with graphical parameters though. You have got the idea, anyway.

Zooming in

We have previously spotted a region of high marker density on the short arm of chromosome 6. Let’s try to have a closer look.

pp <- getDefaultPlotParams(plot.type=1)
pp$leftmargin <- 0.15
pp$topmargin <- 120
to_zoom <- GRanges('chr6', IRanges(start=20e6, end=60e6))
kp <- plotKaryotype(cex=.7, plot.params=pp, zoom = to_zoom) %>% 
  kpAddBaseNumbers(cex=.5) %>% 
  kpAxis(cex=.5, ymin=0) %>%
  kpBars(data=data_counts, y1 = data_counts$y, ymax=max_count)

Well, almost perfect, only the Y axis has disappeared in a mysterious fashion… Do not know whether it is my fault or a feature of karyoploteR. Anyway, now we can see that the highest counts occur roughly between 30-35MBp. It’d be interesting to get gene names in the region together with some annotation.

Attention! There are two additional things I should have done here if it was a true research study:

  • check the exact coords of high density, nt just eyeballing 30-35Mbp,
  • since 23andMe is using hg19 assembly coordinates and Ensembl database is using newer hg38 assembly, (note that hg19 is the immediate predecessor of hg38!), I should have mapped the coords from one to another using, e.g. liftOver. I actually did and the coords for the region of interest are actually close enough not to bother for the purpose of this post.

Hint To find out the names of attributes and filters available in BioMart, go here and once you are done setting them, click on XML.

# Load the neccessary libraries
library("biomaRt")

# Retrieve the data
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
genes <- getBM(attributes=c("ensembl_gene_id", "external_gene_name", "description", "phenotype_description"), 
               filter=c("chromosome_name","start","end"), 
               values = list(chromosome='6', start='30000000', end='35000000'), 
               mart= ensembl)

# Make a nice table
library("knitr")
library("kableExtra")
genes %>% kable("html") %>%
 kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive")) %>%
 scroll_box(height = "500px")
ensembl_gene_id external_gene_name description phenotype_description
ENSG00000204623 ZNRD1ASP zinc ribbon domain containing 1 antisense, pseudogene [Source:HGNC Symbol;Acc:HGNC:13924]
ENSG00000204622 HLA-J major histocompatibility complex, class I, J (pseudogene) [Source:HGNC Symbol;Acc:HGNC:4967]
ENSG00000237669 HCG4P3
ENSG00000232757 ETF1P1 eukaryotic translation termination factor 1 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:3478]
ENSG00000278104 ZNRD1-AS1_1 ZNRD1 antisense RNA 1 conserved region 1 [Source:RFAM;Acc:RF02218]
ENSG00000275856 ZNRD1-AS1_2 ZNRD1 antisense RNA 1 conserved region 2 [Source:RFAM;Acc:RF02219]
ENSG00000066379 ZNRD1 zinc ribbon domain containing 1 [Source:HGNC Symbol;Acc:HGNC:13182]
ENSG00000278773 ZNRD1-AS1_3 ZNRD1 antisense RNA 1 conserved region 3 [Source:RFAM;Acc:RF02220]
ENSG00000204619 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 [Source:HGNC Symbol;Acc:HGNC:9285]
ENSG00000204618 RNF39 ring finger protein 39 [Source:HGNC Symbol;Acc:HGNC:18064]
ENSG00000204616 TRIM31 tripartite motif containing 31 [Source:HGNC Symbol;Acc:HGNC:16289]
ENSG00000231226 TRIM31-AS1 TRIM31 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39761]
ENSG00000252228 SNORA48 Small nucleolar RNA SNORA48 [Source:RFAM;Acc:RF00554]
ENSG00000204614 TRIM40 tripartite motif containing 40 [Source:HGNC Symbol;Acc:HGNC:18736]
ENSG00000204613 TRIM10 tripartite motif containing 10 [Source:HGNC Symbol;Acc:HGNC:10072]
ENSG00000204610 TRIM15 tripartite motif containing 15 [Source:HGNC Symbol;Acc:HGNC:16284]
ENSG00000234127 TRIM26 tripartite motif containing 26 [Source:HGNC Symbol;Acc:HGNC:12962]
ENSG00000233892 PAIP1P1
ENSG00000270604 HCG17 HLA complex group 17 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:31339]
ENSG00000236475 TRIM26BP tripartite motif containing 26B, pseudogene [Source:HGNC Symbol;Acc:HGNC:31338]
ENSG00000243753 HLA-L major histocompatibility complex, class I, L (pseudogene) [Source:HGNC Symbol;Acc:HGNC:4970]
ENSG00000280128 AL662795.2
ENSG00000231074 HCG18 HLA complex group 18 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:31337]
ENSG00000204599 TRIM39 tripartite motif containing 39 [Source:HGNC Symbol;Acc:HGNC:10065]
ENSG00000248167 TRIM39-RPP21 TRIM39-RPP21 readthrough [Source:HGNC Symbol;Acc:HGNC:38845]
ENSG00000241370 RPP21 ribonuclease P/MRP subunit p21 [Source:HGNC Symbol;Acc:HGNC:21300]
ENSG00000224372 HLA-N major histocompatibility complex, class I, N (pseudogene) [Source:HGNC Symbol;Acc:HGNC:19406]
ENSG00000224486 HCG19P
ENSG00000236405 UBQLN1P1 ubiquilin 1 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:21633]
ENSG00000226577 MICC MHC class I polypeptide-related sequence C (pseudogene) [Source:HGNC Symbol;Acc:HGNC:7092]
ENSG00000229068 TMPOP1 thymopoietin pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:21364]
ENSG00000224936 SUCLA2P1 succinate-CoA ligase ADP-forming beta subunit pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:21632]
ENSG00000236603 RANP1 RAN, member RAS oncogene family pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:21631]
ENSG00000204592 HLA-E major histocompatibility complex, class I, E [Source:HGNC Symbol;Acc:HGNC:4962]
ENSG00000235781 LINC02569 long intergenic non-protein coding RNA 2569 [Source:HGNC Symbol;Acc:HGNC:39760]
ENSG00000204590 GNL1 G protein nucleolar 1 (putative) [Source:HGNC Symbol;Acc:HGNC:4413]
ENSG00000204576 PRR3 proline rich 3 [Source:HGNC Symbol;Acc:HGNC:21149]
ENSG00000204574 ABCF1 ATP binding cassette subfamily F member 1 [Source:HGNC Symbol;Acc:HGNC:70]
ENSG00000216101 MIR877 microRNA 877 [Source:HGNC Symbol;Acc:HGNC:33660]
ENSG00000204569 PPP1R10 protein phosphatase 1 regulatory subunit 10 [Source:HGNC Symbol;Acc:HGNC:9284]
ENSG00000204568 MRPS18B mitochondrial ribosomal protein S18B [Source:HGNC Symbol;Acc:HGNC:14516]
ENSG00000137343 ATAT1 alpha tubulin acetyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:21186]
ENSG00000228415 PTMAP1 prothymosin, alpha pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:9624]
ENSG00000204564 C6orf136 chromosome 6 open reading frame 136 [Source:HGNC Symbol;Acc:HGNC:21301]
ENSG00000204560 DHX16 DEAH-box helicase 16 [Source:HGNC Symbol;Acc:HGNC:2739]
ENSG00000146112 PPP1R18 protein phosphatase 1 regulatory subunit 18 [Source:HGNC Symbol;Acc:HGNC:29413]
ENSG00000137404 NRM nurim [Source:HGNC Symbol;Acc:HGNC:8003]
ENSG00000230449 RPL7P4 ribosomal protein L7 pseudogene 4 [Source:HGNC Symbol;Acc:HGNC:21634]
ENSG00000137337 MDC1 mediator of DNA damage checkpoint 1 [Source:HGNC Symbol;Acc:HGNC:21163]
ENSG00000224328 MDC1-AS1 MDC1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39764]
ENSG00000196230 TUBB tubulin beta class I [Source:HGNC Symbol;Acc:HGNC:20778] Multiple benign circumferential skin creases on limbs
ENSG00000196230 TUBB tubulin beta class I [Source:HGNC Symbol;Acc:HGNC:20778] Cortical dysplasia complex with other brain malformations 6
ENSG00000196230 TUBB tubulin beta class I [Source:HGNC Symbol;Acc:HGNC:20778] Circumferential Skin Creases Kunze Type
ENSG00000196230 TUBB tubulin beta class I [Source:HGNC Symbol;Acc:HGNC:20778] SKIN CREASES CONGENITAL SYMMETRIC CIRCUMFERENTIAL 1
ENSG00000272540 AL662797.1
ENSG00000137312 FLOT1 flotillin 1 [Source:HGNC Symbol;Acc:HGNC:3757]
ENSG00000201988 Y_RNA Y RNA [Source:RFAM;Acc:RF00019]
ENSG00000272273 IER3-AS1 IER3 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:53629]
ENSG00000137331 IER3 immediate early response 3 [Source:HGNC Symbol;Acc:HGNC:5392]
ENSG00000263608 RN7SL353P RNA, 7SL, cytoplasmic 353, pseudogene [Source:HGNC Symbol;Acc:HGNC:46369]
ENSG00000228022 HCG20 HLA complex group 20 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:31334]
ENSG00000214894 LINC00243 long intergenic non-protein coding RNA 243 [Source:HGNC Symbol;Acc:HGNC:30956]
ENSG00000237923 LINC02570 long intergenic non-protein coding RNA 2570 [Source:HGNC Symbol;Acc:HGNC:39766]
ENSG00000202241 RN7SKP186 RNA, 7SK small nuclear pseudogene 186 [Source:HGNC Symbol;Acc:HGNC:45910]
ENSG00000237775 DDR1-AS1 DDR1 antisense RNA 1 (head to head) [Source:HGNC Symbol;Acc:HGNC:28694]
ENSG00000204580 DDR1 discoidin domain receptor tyrosine kinase 1 [Source:HGNC Symbol;Acc:HGNC:2730]
ENSG00000284370 MIR4640 microRNA 4640 [Source:HGNC Symbol;Acc:HGNC:41561]
ENSG00000213780 GTF2H4 general transcription factor IIH subunit 4 [Source:HGNC Symbol;Acc:HGNC:4658]
ENSG00000137411 VARS2 valyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:HGNC:21642] Combined oxidative phosphorylation defect type 20
ENSG00000137411 VARS2 valyl-tRNA synthetase 2, mitochondrial [Source:HGNC Symbol;Acc:HGNC:21642] Combined oxidative phosphorylation deficiency 20
ENSG00000196260 SFTA2 surfactant associated 2 [Source:HGNC Symbol;Acc:HGNC:18386]
ENSG00000252761 Y_RNA Y RNA [Source:RFAM;Acc:RF00019]
ENSG00000168631 DPCR1 diffuse panbronchiolitis critical region 1 [Source:HGNC Symbol;Acc:HGNC:21666] Diffuse panbronchiolitis
ENSG00000233529 HCG21 HLA complex group 21 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:31335]
ENSG00000275906 NAPGP2 N-ethylmaleimide-sensitive factor attachment protein, gamma pseudogene 2 [Source:HGNC Symbol;Acc:HGNC:45166]
ENSG00000204544 MUC21 mucin 21, cell surface associated [Source:HGNC Symbol;Acc:HGNC:21661]
ENSG00000261272 MUC22 mucin 22 [Source:HGNC Symbol;Acc:HGNC:39755]
ENSG00000228789 HCG22 HLA complex group 22 (gene/pseudogene) [Source:HGNC Symbol;Acc:HGNC:27780]
ENSG00000222895 RNU6-1133P RNA, U6 small nuclear 1133, pseudogene [Source:HGNC Symbol;Acc:HGNC:48096]
ENSG00000204542 C6orf15 chromosome 6 open reading frame 15 [Source:HGNC Symbol;Acc:HGNC:13927]
ENSG00000204540 PSORS1C1 psoriasis susceptibility 1 candidate 1 [Source:HGNC Symbol;Acc:HGNC:17202]
ENSG00000204539 CDSN corneodesmosin [Source:HGNC Symbol;Acc:HGNC:1802] Hypotrichosis simplex of the scalp
ENSG00000204539 CDSN corneodesmosin [Source:HGNC Symbol;Acc:HGNC:1802] Generalized peeling skin syndrome type B
ENSG00000204539 CDSN corneodesmosin [Source:HGNC Symbol;Acc:HGNC:1802] HYPOTRICHOSIS 2
ENSG00000204539 CDSN corneodesmosin [Source:HGNC Symbol;Acc:HGNC:1802] PEELING SKIN SYNDROME 1
ENSG00000204538 PSORS1C2 psoriasis susceptibility 1 candidate 2 [Source:HGNC Symbol;Acc:HGNC:17199]
ENSG00000238211 POLR2LP1 RNA polymerase II subunit L pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:31340]
ENSG00000204536 CCHCR1 coiled-coil alpha-helical rod protein 1 [Source:HGNC Symbol;Acc:HGNC:13930]
ENSG00000137310 TCF19 transcription factor 19 [Source:HGNC Symbol;Acc:HGNC:11629]
ENSG00000204531 POU5F1 POU class 5 homeobox 1 [Source:HGNC Symbol;Acc:HGNC:9221]
ENSG00000204528 PSORS1C3 psoriasis susceptibility 1 candidate 3 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:17203]
ENSG00000272501 AL662844.4
ENSG00000206344 HCG27 HLA complex group 27 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:27366]
ENSG00000271821 AL662844.3
ENSG00000255726 AL662844.1
ENSG00000255899 AL662844.2
ENSG00000204525 HLA-C major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933] Precursor B-cell acute lymphoblastic leukemia
ENSG00000204525 HLA-C major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933] HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUSCEPTIBILITY TO
ENSG00000204525 HLA-C major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933] PSORIASIS 1 SUSCEPTIBILITY TO
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] Abacavir toxicity
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] Allopurinol toxicity
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] Flucloxacilline toxicity
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] Phenytoin or carbamazepine toxicity
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] Pulmonary arterial hypertension associated with connective tissue disease
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] Stevens-Johnson syndrome
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] Takayasu arteritis
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] SEVERE CUTANEOUS ADVERSE REACTION SUSCEPTIBILITY TO TOXIC EPIDERMAL NECROLYSIS SUSCEPTIBILITY TO INCLUDED
ENSG00000234745 HLA-B major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932] SPONDYLOARTHROPATHY SUSCEPTIBILITY TO 1
ENSG00000214892 USP8P1 ubiquitin specific peptidase 8 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:13987]
ENSG00000227939 RPL3P2 ribosomal protein L3 pseudogene 2 [Source:HGNC Symbol;Acc:HGNC:17834]
ENSG00000231402 WASF5P WAS protein family member 5, pseudogene [Source:HGNC Symbol;Acc:HGNC:21665]
ENSG00000256166 LINC02571 long intergenic non-protein coding RNA 2571 [Source:HGNC Symbol;Acc:HGNC:53630]
ENSG00000229836 AL671883.1
ENSG00000277402 MIR6891 microRNA 6891 [Source:HGNC Symbol;Acc:HGNC:50243]
ENSG00000271581 AL671883.2
ENSG00000228432 DHFRP2 dihydrofolate reductase pseudogene 2 [Source:HGNC Symbol;Acc:HGNC:2863]
ENSG00000201658 RNU6-283P RNA, U6 small nuclear 283, pseudogene [Source:HGNC Symbol;Acc:HGNC:47246]
ENSG00000230994 FGFR3P1 fibroblast growth factor receptor 3 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:21664]
ENSG00000223702 ZDHHC20P2 zinc finger DHHC-type containing 20 pseudogene 2 [Source:HGNC Symbol;Acc:HGNC:33457]
ENSG00000225851 HLA-S major histocompatibility complex, class I, S (pseudogene) [Source:HGNC Symbol;Acc:HGNC:19395]
ENSG00000272221 AL645933.2
ENSG00000204520 MICA MHC class I polypeptide-related sequence A [Source:HGNC Symbol;Acc:HGNC:7090]
ENSG00000206337 HCP5 HLA complex P5 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:21659]
ENSG00000199332 Y_RNA Y RNA [Source:RFAM;Acc:RF00019]
ENSG00000230174 LINC01149 long intergenic non-protein coding RNA 1149 [Source:HGNC Symbol;Acc:HGNC:39757]
ENSG00000233902 AL645933.1
ENSG00000204516 MICB MHC class I polypeptide-related sequence B [Source:HGNC Symbol;Acc:HGNC:7091]
ENSG00000201680 Y_RNA Y RNA [Source:RFAM;Acc:RF00019]
ENSG00000256851 AL663061.2
ENSG00000219797 PPIAP9 peptidylprolyl isomerase A pseudogene 9 [Source:HGNC Symbol;Acc:HGNC:9272]
ENSG00000225499 RPL15P4
ENSG00000204511 MCCD1 mitochondrial coiled-coil domain 1 [Source:HGNC Symbol;Acc:HGNC:20668]
ENSG00000198563 DDX39B DExD-box helicase 39B [Source:HGNC Symbol;Acc:HGNC:13917]
ENSG00000254870 ATP6V1G2-DDX39B ATP6V1G2-DDX39B readthrough (NMD candidate) [Source:HGNC Symbol;Acc:HGNC:41999]
ENSG00000201785 SNORD117 small nucleolar RNA, C/D box 117 [Source:HGNC Symbol;Acc:HGNC:32742]
ENSG00000265236 SNORD84 small nucleolar RNA, C/D box 84 [Source:HGNC Symbol;Acc:HGNC:32743]
ENSG00000234006 DDX39B-AS1 DDX39B antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39771]
ENSG00000213760 ATP6V1G2 ATPase H+ transporting V1 subunit G2 [Source:HGNC Symbol;Acc:HGNC:862]
ENSG00000204498 NFKBIL1 NFKB inhibitor like 1 [Source:HGNC Symbol;Acc:HGNC:7800]
ENSG00000226979 LTA lymphotoxin alpha [Source:HGNC Symbol;Acc:HGNC:6709] LEPROSY SUSCEPTIBILITY TO 4
ENSG00000226979 LTA lymphotoxin alpha [Source:HGNC Symbol;Acc:HGNC:6709] MYOCARDIAL INFARCTION SUSCEPTIBILITY TO MYOCARDIAL INFARCTION SUSCEPTIBILITY TO 1 INCLUDED
ENSG00000226979 LTA lymphotoxin alpha [Source:HGNC Symbol;Acc:HGNC:6709] PSORIATIC ARTHRITIS SUSCEPTIBILITY TOPSORIATIC ARTHRITIS SUSCEPTIBILITY TO 1 INCLUDED
ENSG00000232810 TNF tumor necrosis factor [Source:HGNC Symbol;Acc:HGNC:11892] ASTHMA SUSCEPTIBILITY TO
ENSG00000232810 TNF tumor necrosis factor [Source:HGNC Symbol;Acc:HGNC:11892] MALARIA SUSCEPTIBILITY TO MALARIA RESISTANCE TO INCLUDED
ENSG00000232810 TNF tumor necrosis factor [Source:HGNC Symbol;Acc:HGNC:11892] MIGRAINE WITH OR WITHOUT AURA SUSCEPTIBILITY TO 1
ENSG00000227507 LTB lymphotoxin beta [Source:HGNC Symbol;Acc:HGNC:6711]
ENSG00000204482 LST1 leukocyte specific transcript 1 [Source:HGNC Symbol;Acc:HGNC:14189]
ENSG00000204475 NCR3 natural cytotoxicity triggering receptor 3 [Source:HGNC Symbol;Acc:HGNC:19077] MALARIA MILD SUSCEPTIBILITY TO
ENSG00000230622 UQCRHP1 ubiquinol-cytochrome c reductase hinge protein pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:31341]
ENSG00000204472 AIF1 allograft inflammatory factor 1 [Source:HGNC Symbol;Acc:HGNC:352]
ENSG00000204469 PRRC2A proline rich coiled-coil 2A [Source:HGNC Symbol;Acc:HGNC:13918]
ENSG00000200816 SNORA38 small nucleolar RNA, H/ACA box 38 [Source:HGNC Symbol;Acc:HGNC:32631]
ENSG00000274494 MIR6832 microRNA 6832 [Source:HGNC Symbol;Acc:HGNC:50140]
ENSG00000204463 BAG6 BCL2 associated athanogene 6 [Source:HGNC Symbol;Acc:HGNC:13919]
ENSG00000204444 APOM apolipoprotein M [Source:HGNC Symbol;Acc:HGNC:13916]
ENSG00000204439 C6orf47 chromosome 6 open reading frame 47 [Source:HGNC Symbol;Acc:HGNC:19076]
ENSG00000227198 C6orf47-AS1 C6orf47 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39767]
ENSG00000204438 GPANK1 G-patch domain and ankyrin repeats 1 [Source:HGNC Symbol;Acc:HGNC:13920]
ENSG00000201207 Y_RNA Y RNA [Source:RFAM;Acc:RF00019]
ENSG00000204435 CSNK2B casein kinase 2 beta [Source:HGNC Symbol;Acc:HGNC:2460]
ENSG00000263020 AL662899.2
ENSG00000240053 LY6G5B lymphocyte antigen 6 family member G5B [Source:HGNC Symbol;Acc:HGNC:13931]
ENSG00000204428 LY6G5C lymphocyte antigen 6 family member G5C [Source:HGNC Symbol;Acc:HGNC:13932]
ENSG00000204427 ABHD16A abhydrolase domain containing 16A [Source:HGNC Symbol;Acc:HGNC:13921]
ENSG00000204422 AL662899.1
ENSG00000266776 MIR4646 microRNA 4646 [Source:HGNC Symbol;Acc:HGNC:41543]
ENSG00000204424 LY6G6F lymphocyte antigen 6 family member G6F [Source:HGNC Symbol;Acc:HGNC:13933]
ENSG00000250641 LY6G6F-LY6G6D LY6G6F-LY6G6D readthrough [Source:NCBI gene;Acc:110599563]
ENSG00000255552 LY6G6E lymphocyte antigen 6 family member G6E [Source:HGNC Symbol;Acc:HGNC:13934]
ENSG00000244355 LY6G6D lymphocyte antigen 6 family member G6D [Source:HGNC Symbol;Acc:HGNC:13935]
ENSG00000204420 MPIG6B megakaryocyte and platelet inhibitory receptor G6b [Source:HGNC Symbol;Acc:HGNC:13937] THROMBOCYTOPENIA ANEMIA AND MYELOFIBROSIS
ENSG00000204421 LY6G6C lymphocyte antigen 6 family member G6C [Source:HGNC Symbol;Acc:HGNC:13936]
ENSG00000213722 DDAH2 dimethylarginine dimethylaminohydrolase 2 [Source:HGNC Symbol;Acc:HGNC:2716]
ENSG00000213719 CLIC1 chloride intracellular channel 1 [Source:HGNC Symbol;Acc:HGNC:2062]
ENSG00000204410 MSH5 mutS homolog 5 [Source:HGNC Symbol;Acc:HGNC:7328] PREMATURE OVARIAN FAILURE 13
ENSG00000255152 MSH5-SAPCD1 MSH5-SAPCD1 readthrough (NMD candidate) [Source:HGNC Symbol;Acc:HGNC:41994]
ENSG00000252743 RNU6-850P RNA, U6 small nuclear 850, pseudogene [Source:HGNC Symbol;Acc:HGNC:47813]
ENSG00000228727 SAPCD1 suppressor APC domain containing 1 [Source:HGNC Symbol;Acc:HGNC:13938]
ENSG00000235663 SAPCD1-AS1 SAPCD1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39824]
ENSG00000204396 VWA7 von Willebrand factor A domain containing 7 [Source:HGNC Symbol;Acc:HGNC:13939]
ENSG00000204394 VARS valyl-tRNA synthetase [Source:HGNC Symbol;Acc:HGNC:12651]
ENSG00000201555 Y_RNA Y RNA [Source:RFAM;Acc:RF00019]
ENSG00000204392 LSM2 LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated [Source:HGNC Symbol;Acc:HGNC:13940]
ENSG00000204390 HSPA1L heat shock protein family A (Hsp70) member 1 like [Source:HGNC Symbol;Acc:HGNC:5234]
ENSG00000204389 HSPA1A heat shock protein family A (Hsp70) member 1A [Source:HGNC Symbol;Acc:HGNC:5232]
ENSG00000204388 HSPA1B heat shock protein family A (Hsp70) member 1B [Source:HGNC Symbol;Acc:HGNC:5233]
ENSG00000204387 C6orf48 chromosome 6 open reading frame 48 [Source:HGNC Symbol;Acc:HGNC:19078]
ENSG00000201823 SNORD48 small nucleolar RNA, C/D box 48 [Source:HGNC Symbol;Acc:HGNC:10188]
ENSG00000201754 SNORD52 small nucleolar RNA, C/D box 52 [Source:HGNC Symbol;Acc:HGNC:10202]
ENSG00000204386 NEU1 neuraminidase 1 [Source:HGNC Symbol;Acc:HGNC:7758] Congenital sialidosis type 2
ENSG00000204386 NEU1 neuraminidase 1 [Source:HGNC Symbol;Acc:HGNC:7758] Juvenile sialidosis type 2
ENSG00000204386 NEU1 neuraminidase 1 [Source:HGNC Symbol;Acc:HGNC:7758] Sialidosis type 1
ENSG00000204386 NEU1 neuraminidase 1 [Source:HGNC Symbol;Acc:HGNC:7758] Sialidosis
ENSG00000204386 NEU1 neuraminidase 1 [Source:HGNC Symbol;Acc:HGNC:7758] NEURAMINIDASE DEFICIENCY
ENSG00000204385 SLC44A4 solute carrier family 44 member 4 [Source:HGNC Symbol;Acc:HGNC:13941] Autosomal dominant nonsyndromic sensorineural deafness type DFNA
ENSG00000204385 SLC44A4 solute carrier family 44 member 4 [Source:HGNC Symbol;Acc:HGNC:13941] DEAFNESS AUTOSOMAL DOMINANT 72
ENSG00000204371 EHMT2 euchromatic histone lysine methyltransferase 2 [Source:HGNC Symbol;Acc:HGNC:14129]
ENSG00000237080 EHMT2-AS1 EHMT2 and SLC44A4 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39751]
ENSG00000166278 C2 complement C2 [Source:HGNC Symbol;Acc:HGNC:1248] Immunodeficiency due to a classical component pathway complement deficiency
ENSG00000166278 C2 complement C2 [Source:HGNC Symbol;Acc:HGNC:1248] COMPLEMENT COMPONENT 2 DEFICIENCY
ENSG00000166278 C2 complement C2 [Source:HGNC Symbol;Acc:HGNC:1248] MACULAR DEGENERATION AGE-RELATED 14 REDUCED RISK OF
ENSG00000204366 ZBTB12 zinc finger and BTB domain containing 12 [Source:HGNC Symbol;Acc:HGNC:19066]
ENSG00000244255 AL645922.1
ENSG00000281756 C2-AS1 C2 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:49464]
ENSG00000243649 CFB complement factor B [Source:HGNC Symbol;Acc:HGNC:1037] Atypical hemolytic uremic syndrome with B factor anomaly
ENSG00000243649 CFB complement factor B [Source:HGNC Symbol;Acc:HGNC:1037] COMPLEMENT FACTOR B DEFICIENCY
ENSG00000243649 CFB complement factor B [Source:HGNC Symbol;Acc:HGNC:1037] HEMOLYTIC UREMIC SYNDROME ATYPICAL SUSCEPTIBILITY TO 4
ENSG00000243649 CFB complement factor B [Source:HGNC Symbol;Acc:HGNC:1037] MACULAR DEGENERATION AGE-RELATED 14 REDUCED RISK OF
ENSG00000204356 NELFE negative elongation factor complex member E [Source:HGNC Symbol;Acc:HGNC:13974]
ENSG00000284446 MIR1236 microRNA 1236 [Source:HGNC Symbol;Acc:HGNC:33925]
ENSG00000204351 SKIV2L Ski2 like RNA helicase [Source:HGNC Symbol;Acc:HGNC:10898] Syndromic diarrhea
ENSG00000204351 SKIV2L Ski2 like RNA helicase [Source:HGNC Symbol;Acc:HGNC:10898] TRICHOHEPATOENTERIC SYNDROME 2
ENSG00000204348 DXO decapping exoribonuclease [Source:HGNC Symbol;Acc:HGNC:2992]
ENSG00000204344 STK19 serine/threonine kinase 19 [Source:HGNC Symbol;Acc:HGNC:11398]
ENSG00000244731 C4A complement C4A (Rodgers blood group) [Source:HGNC Symbol;Acc:HGNC:1323] Autosomal systemic lupus erythematosus
ENSG00000244731 C4A complement C4A (Rodgers blood group) [Source:HGNC Symbol;Acc:HGNC:1323] Immunodeficiency due to a classical component pathway complement deficiency
ENSG00000244731 C4A complement C4A (Rodgers blood group) [Source:HGNC Symbol;Acc:HGNC:1323] BLOOD GROUP CHIDO/RODGERS SYSTEM
ENSG00000244731 C4A complement C4A (Rodgers blood group) [Source:HGNC Symbol;Acc:HGNC:1323] COMPLEMENT COMPONENT 4A DEFICIENCY
ENSG00000233627 C4A-AS1 C4A antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39753]
ENSG00000204338 CYP21A1P cytochrome P450 family 21 subfamily A member 1, pseudogene [Source:HGNC Symbol;Acc:HGNC:2599]
ENSG00000248290 TNXA tenascin XA (pseudogene) [Source:HGNC Symbol;Acc:HGNC:11975]
ENSG00000250535 STK19B serine/threonine kinase 19B (pseudogene) [Source:HGNC Symbol;Acc:HGNC:21668]
ENSG00000224389 C4B complement C4B (Chido blood group) [Source:HGNC Symbol;Acc:HGNC:1324] Immunodeficiency due to a classical component pathway complement deficiency
ENSG00000224389 C4B complement C4B (Chido blood group) [Source:HGNC Symbol;Acc:HGNC:1324] COMPLEMENT COMPONENT 4B DEFICIENCY
ENSG00000229776 C4B-AS1 C4B antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39752]
ENSG00000231852 CYP21A2 cytochrome P450 family 21 subfamily A member 2 [Source:HGNC Symbol;Acc:HGNC:2600] Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency salt wasting form
ENSG00000231852 CYP21A2 cytochrome P450 family 21 subfamily A member 2 [Source:HGNC Symbol;Acc:HGNC:2600] Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency simple virilizing form
ENSG00000231852 CYP21A2 cytochrome P450 family 21 subfamily A member 2 [Source:HGNC Symbol;Acc:HGNC:2600] ADRENAL HYPERPLASIA CONGENITAL DUE TO 21-HYDROXYLASE DEFICIENCY
ENSG00000168477 TNXB tenascin XB [Source:HGNC Symbol;Acc:HGNC:11976] Ehlers-Danlos syndrome due to tenascin-X deficiency
ENSG00000168477 TNXB tenascin XB [Source:HGNC Symbol;Acc:HGNC:11976] EHLERS-DANLOS SYNDROME HYPERMOBILITY TYPE
ENSG00000168477 TNXB tenascin XB [Source:HGNC Symbol;Acc:HGNC:11976] Familial vesicoureteral reflux
ENSG00000168477 TNXB tenascin XB [Source:HGNC Symbol;Acc:HGNC:11976] Vesicoureteral reflux 8
ENSG00000252512 RNA5SP206 RNA, 5S ribosomal pseudogene 206 [Source:HGNC Symbol;Acc:HGNC:43106]
ENSG00000213676 ATF6B activating transcription factor 6 beta [Source:HGNC Symbol;Acc:HGNC:2349]
ENSG00000204315 FKBPL FK506 binding protein like [Source:HGNC Symbol;Acc:HGNC:13949]
ENSG00000204314 PRRT1 proline rich transmembrane protein 1 [Source:HGNC Symbol;Acc:HGNC:13943]
ENSG00000221988 PPT2 palmitoyl-protein thioesterase 2 [Source:HGNC Symbol;Acc:HGNC:9326]
ENSG00000258388 PPT2-EGFL8 PPT2-EGFL8 readthrough (NMD candidate) [Source:HGNC Symbol;Acc:HGNC:48343]
ENSG00000241404 EGFL8 EGF like domain multiple 8 [Source:HGNC Symbol;Acc:HGNC:13944]
ENSG00000204310 AGPAT1 1-acylglycerol-3-phosphate O-acyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:324]
ENSG00000284469 MIR6721 microRNA 6721 [Source:HGNC Symbol;Acc:HGNC:50049]
ENSG00000204308 RNF5 ring finger protein 5 [Source:HGNC Symbol;Acc:HGNC:10068]
ENSG00000277264 MIR6833 microRNA 6833 [Source:HGNC Symbol;Acc:HGNC:50245]
ENSG00000204305 AGER advanced glycosylation end-product specific receptor [Source:HGNC Symbol;Acc:HGNC:320]
ENSG00000273333 AL662884.1
ENSG00000204304 PBX2 PBX homeobox 2 [Source:HGNC Symbol;Acc:HGNC:8633]
ENSG00000213654 GPSM3 G protein signaling modulator 3 [Source:HGNC Symbol;Acc:HGNC:13945]
ENSG00000204301 NOTCH4 notch 4 [Source:HGNC Symbol;Acc:HGNC:7884]
ENSG00000277427 AL671511.2
ENSG00000225914 AL671511.1
ENSG00000204296 C6orf10 chromosome 6 open reading frame 10 [Source:HGNC Symbol;Acc:HGNC:13922]
ENSG00000237285 HNRNPA1P2 heterogeneous nuclear ribonucleoprotein A1 pseudogene 2 [Source:HGNC Symbol;Acc:HGNC:13958]
ENSG00000223335 RNU6-603P RNA, U6 small nuclear 603, pseudogene [Source:HGNC Symbol;Acc:HGNC:47566]
ENSG00000228962 HCG23 HLA complex group 23 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:19713]
ENSG00000204290 BTNL2 butyrophilin like 2 [Source:HGNC Symbol;Acc:HGNC:1142] Sarcoidosis
ENSG00000204290 BTNL2 butyrophilin like 2 [Source:HGNC Symbol;Acc:HGNC:1142] SARCOIDOSIS SUSCEPTIBILITY TO 2
ENSG00000204287 HLA-DRA major histocompatibility complex, class II, DR alpha [Source:HGNC Symbol;Acc:HGNC:4947] Graham Little-Piccardi-Lassueur syndrome
ENSG00000196301 HLA-DRB9 major histocompatibility complex, class II, DR beta 9 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:4957]
ENSG00000198502 HLA-DRB5 major histocompatibility complex, class II, DR beta 5 [Source:HGNC Symbol;Acc:HGNC:4953]
ENSG00000251916 RNU1-61P RNA, U1 small nuclear 61, pseudogene [Source:HGNC Symbol;Acc:HGNC:48403]
ENSG00000229391 HLA-DRB6 major histocompatibility complex, class II, DR beta 6 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:4954]
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Bullous pemphigoid
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Diffuse cutaneous systemic sclerosis
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Follicular lymphoma
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Limbic encephalitis with LGI1 antibodies
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Limited cutaneous systemic sclerosis
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Limited systemic sclerosis
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Narcolepsy without cataplexy
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Narcolepsy-cataplexy syndrome
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Pediatric multiple sclerosis
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Sarcoidosis
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] Systemic-onset juvenile idiopathic arthritis
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] MULTIPLE SCLEROSIS SUSCEPTIBILITY TO 5
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] RHEUMATOID ARTHRITIS
ENSG00000196126 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 [Source:HGNC Symbol;Acc:HGNC:4948] SARCOIDOSIS SUSCEPTIBILITY TO 1
ENSG00000196735 HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 [Source:HGNC Symbol;Acc:HGNC:4942] Adult-onset myasthenia gravis
ENSG00000196735 HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 [Source:HGNC Symbol;Acc:HGNC:4942] Idiopathic achalasia
ENSG00000196735 HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 [Source:HGNC Symbol;Acc:HGNC:4942] CELIAC DISEASE SUSCEPTIBILITY TO 13
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] Bullous pemphigoid
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] Idiopathic achalasia
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] Limbic encephalitis with LGI1 antibodies
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] Narcolepsy without cataplexy
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] Narcolepsy-cataplexy syndrome
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] Pediatric multiple sclerosis
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] CELIAC DISEASE SUSCEPTIBILITY TO 13
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] CREUTZFELDT-JAKOB DISEASE
ENSG00000179344 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944] MULTIPLE SCLEROSIS SUSCEPTIBILITY TO 5
ENSG00000223534 HLA-DQB1-AS1 HLA-DQB1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:39762]
ENSG00000235040 MTCO3P1 mitochondrially encoded cytochrome c oxidase III pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:31342]
ENSG00000232080 AL662789.1
ENSG00000226030 HLA-DQB3 major histocompatibility complex, class II, DQ beta 3 [Source:HGNC Symbol;Acc:HGNC:4946]
ENSG00000237541 HLA-DQA2 major histocompatibility complex, class II, DQ alpha 2 [Source:HGNC Symbol;Acc:HGNC:4943]
ENSG00000263649 MIR3135B microRNA 3135b [Source:HGNC Symbol;Acc:HGNC:41783]
ENSG00000232629 HLA-DQB2 major histocompatibility complex, class II, DQ beta 2 [Source:HGNC Symbol;Acc:HGNC:4945]
ENSG00000241106 HLA-DOB major histocompatibility complex, class II, DO beta [Source:HGNC Symbol;Acc:HGNC:4937]
ENSG00000250264 AL669918.1
ENSG00000204267 TAP2 transporter 2, ATP binding cassette subfamily B member [Source:HGNC Symbol;Acc:HGNC:44] Immunodeficiency by defective expression of HLA class 1
ENSG00000204267 TAP2 transporter 2, ATP binding cassette subfamily B member [Source:HGNC Symbol;Acc:HGNC:44] BARE LYMPHOCYTE SYNDROME TYPE II COMPLEMENTATION GROUP D
ENSG00000204264 PSMB8 proteasome subunit beta 8 [Source:HGNC Symbol;Acc:HGNC:9545] CANDLE syndrome
ENSG00000204264 PSMB8 proteasome subunit beta 8 [Source:HGNC Symbol;Acc:HGNC:9545] JMP syndrome
ENSG00000204264 PSMB8 proteasome subunit beta 8 [Source:HGNC Symbol;Acc:HGNC:9545] Nakajo-Nishimura syndrome
ENSG00000204264 PSMB8 proteasome subunit beta 8 [Source:HGNC Symbol;Acc:HGNC:9545] Nakajo syndrome
ENSG00000204264 PSMB8 proteasome subunit beta 8 [Source:HGNC Symbol;Acc:HGNC:9545] AUTOINFLAMMATION LIPODYSTROPHY AND DERMATOSIS SYNDROME
ENSG00000204261 PSMB8-AS1 PSMB8 antisense RNA 1 (head to head) [Source:HGNC Symbol;Acc:HGNC:39758]
ENSG00000240065 PSMB9 proteasome subunit beta 9 [Source:HGNC Symbol;Acc:HGNC:9546]
ENSG00000168394 TAP1 transporter 1, ATP binding cassette subfamily B member [Source:HGNC Symbol;Acc:HGNC:43] Immunodeficiency by defective expression of HLA class 1
ENSG00000168394 TAP1 transporter 1, ATP binding cassette subfamily B member [Source:HGNC Symbol;Acc:HGNC:43] BARE LYMPHOCYTE SYNDROME TYPE II COMPLEMENTATION GROUP D
ENSG00000234515 PPP1R2P1 protein phosphatase 1 regulatory inhibitor subunit 2 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:9289]
ENSG00000235301 HLA-Z major histocompatibility complex, class I, Z (pseudogene) [Source:HGNC Symbol;Acc:HGNC:19394]
ENSG00000242574 HLA-DMB major histocompatibility complex, class II, DM beta [Source:HGNC Symbol;Acc:HGNC:4935]
ENSG00000248993 AL645941.2
ENSG00000204257 HLA-DMA major histocompatibility complex, class II, DM alpha [Source:HGNC Symbol;Acc:HGNC:4934]
ENSG00000204256 BRD2 bromodomain containing 2 [Source:HGNC Symbol;Acc:HGNC:1103]
ENSG00000223837 AL645941.1
ENSG00000263756 AL645941.3
ENSG00000204252 HLA-DOA major histocompatibility complex, class II, DO alpha [Source:HGNC Symbol;Acc:HGNC:4936]
ENSG00000231389 HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 [Source:HGNC Symbol;Acc:HGNC:4938]
ENSG00000223865 HLA-DPB1 major histocompatibility complex, class II, DP beta 1 [Source:HGNC Symbol;Acc:HGNC:4940] Chronic beryllium disease
ENSG00000223865 HLA-DPB1 major histocompatibility complex, class II, DP beta 1 [Source:HGNC Symbol;Acc:HGNC:4940] Granulomatosis with polyangiitis
ENSG00000224796 RPL32P1
ENSG00000231461 HLA-DPA2 major histocompatibility complex, class II, DP alpha 2 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:4939]
ENSG00000228688 COL11A2P1 collagen type XI alpha 2 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:13947]
ENSG00000224557 HLA-DPB2 major histocompatibility complex, class II, DP beta 2 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:4941]
ENSG00000237398 HLA-DPA3 major histocompatibility complex, class II, DP alpha 3 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:19393]
ENSG00000230313 HCG24 HLA complex group 24 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:23500]
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] Autosomal dominant nonsyndromic sensorineural deafness type DFNA
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] Autosomal recessive non-syndromic sensorineural deafness type DFNB
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] Fibrochondrogenesis
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] OTOSPONDYLOMEGAEPIPHYSEAL DYSPLASIA
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] Stickler syndrome type 3 (STL3)
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] Weissenbacher-Zweymuller syndrome
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] autosomal recessive otospondylomegaepiphyseal dysplasia (OSMED)
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] deafness autosomal dominant type 13 (DFNA13)
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] deafness autosomal recessive type 53 (DFNB53)
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] Weissenbacher-Zweymueller syndrome (WZS)
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] DEAFNESS AUTOSOMAL DOMINANT 13
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] DEAFNESS AUTOSOMAL RECESSIVE 53
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] FIBROCHONDROGENESIS 2
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] OTOSPONDYLOMEGAEPIPHYSEAL DYSPLASIA AUTOSOMAL DOMINANT
ENSG00000204248 COL11A2 collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187] OTOSPONDYLOMEGAEPIPHYSEAL DYSPLASIA AUTOSOMAL RECESSIVE
ENSG00000204231 RXRB retinoid X receptor beta [Source:HGNC Symbol;Acc:HGNC:10478]
ENSG00000202441 RNY4P10 RNA, Ro-associated Y4 pseudogene 10 [Source:HGNC Symbol;Acc:HGNC:34060]
ENSG00000112473 SLC39A7 solute carrier family 39 member 7 [Source:HGNC Symbol;Acc:HGNC:4927]
ENSG00000204228 HSD17B8 hydroxysteroid 17-beta dehydrogenase 8 [Source:HGNC Symbol;Acc:HGNC:3554]
ENSG00000199036 MIR219A1 microRNA 219a-1 [Source:HGNC Symbol;Acc:HGNC:31597]
ENSG00000204227 RING1 ring finger protein 1 [Source:HGNC Symbol;Acc:HGNC:10018]
ENSG00000225463 ZNF70P1 zinc finger protein 70 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:13846]
ENSG00000223457 HTATSF1P1 HIV-1 Tat specific factor 1 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:13959]
ENSG00000272217 AL645940.1
ENSG00000232940 HCG25 HLA complex group 25 (non-protein coding) [Source:HGNC Symbol;Acc:HGNC:20196]
ENSG00000223501 VPS52 VPS52, GARP complex subunit [Source:HGNC Symbol;Acc:HGNC:10518]
ENSG00000231500 RPS18 ribosomal protein S18 [Source:HGNC Symbol;Acc:HGNC:10401]
ENSG00000235863 B3GALT4 beta-1,3-galactosyltransferase 4 [Source:HGNC Symbol;Acc:HGNC:919]
ENSG00000227057 WDR46 WD repeat domain 46 [Source:HGNC Symbol;Acc:HGNC:13923]
ENSG00000284517 MIR6873 microRNA 6873 [Source:HGNC Symbol;Acc:HGNC:50231]
ENSG00000204220 PFDN6 prefoldin subunit 6 [Source:HGNC Symbol;Acc:HGNC:4926]
ENSG00000284064 MIR6834 microRNA 6834 [Source:HGNC Symbol;Acc:HGNC:50108]
ENSG00000237441 RGL2 ral guanine nucleotide dissociation stimulator like 2 [Source:HGNC Symbol;Acc:HGNC:9769]
ENSG00000231925 TAPBP TAP binding protein [Source:HGNC Symbol;Acc:HGNC:11566] Immunodeficiency by defective expression of HLA class 1
ENSG00000231925 TAPBP TAP binding protein [Source:HGNC Symbol;Acc:HGNC:11566] BARE LYMPHOCYTE SYNDROME TYPE II COMPLEMENTATION GROUP D
ENSG00000236104 ZBTB22 zinc finger and BTB domain containing 22 [Source:HGNC Symbol;Acc:HGNC:13085]
ENSG00000204209 DAXX death domain associated protein [Source:HGNC Symbol;Acc:HGNC:2681] Gastric neuroendocrine tumor
ENSG00000229596 MYL8P myosin light chain 8, pseudogene [Source:HGNC Symbol;Acc:HGNC:7589]
ENSG00000228285 LYPLA2P1 lysophospholipase II pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:21069]
ENSG00000225644 RPL35AP4 ribosomal protein L35a pseudogene 4 [Source:HGNC Symbol;Acc:HGNC:33460]
ENSG00000237649 KIFC1 kinesin family member C1 [Source:HGNC Symbol;Acc:HGNC:6389]
ENSG00000204194 RPL12P1 ribosomal protein L12 pseudogene 1 [Source:HGNC Symbol;Acc:HGNC:13976]
ENSG00000112511 PHF1 PHD finger protein 1 [Source:HGNC Symbol;Acc:HGNC:8919]
ENSG00000112514 CUTA cutA divalent cation tolerance homolog [Source:HGNC Symbol;Acc:HGNC:21101]
ENSG00000197283 SYNGAP1 synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497] Autosomal dominant non-syndromic intellectual disability
ENSG00000197283 SYNGAP1 synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497] Undetermined early-onset epileptic encephalopathy
ENSG00000197283 SYNGAP1 synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497] Epileptic encephalopathy
ENSG00000197283 SYNGAP1 synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497] mental retardation autosomal dominant type 5 (MRD5)
ENSG00000197283 SYNGAP1 synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:HGNC:11497] MENTAL RETARDATION AUTOSOMAL DOMINANT 5
ENSG00000274259 AL662799.1
ENSG00000284256 MIR5004 microRNA 5004 [Source:HGNC Symbol;Acc:HGNC:43532]
ENSG00000213588 ZBTB9 zinc finger and BTB domain containing 9 [Source:HGNC Symbol;Acc:HGNC:28323]
ENSG00000204188 GGNBP1 gametogenetin binding protein 1 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:19427]
ENSG00000242014 RN7SL26P RNA, 7SL, cytoplasmic 26, pseudogene [Source:HGNC Symbol;Acc:HGNC:46042]
ENSG00000276746 Metazoa_SRP Metazoan signal recognition particle RNA [Source:RFAM;Acc:RF00017]
ENSG00000030110 BAK1 BCL2 antagonist/killer 1 [Source:HGNC Symbol;Acc:HGNC:949]
ENSG00000197251 LINC00336 long intergenic non-protein coding RNA 336 [Source:HGNC Symbol;Acc:HGNC:33813]
ENSG00000096433 ITPR3 inositol 1,4,5-trisphosphate receptor type 3 [Source:HGNC Symbol;Acc:HGNC:6182] DIABETES MELLITUS INSULIN-DEPENDENT 19
ENSG00000137288 UQCC2 ubiquinol-cytochrome c reductase complex assembly factor 2 [Source:HGNC Symbol;Acc:HGNC:21237] Isolated CoQ-cytochrome C reductase deficiency
ENSG00000137288 UQCC2 ubiquinol-cytochrome c reductase complex assembly factor 2 [Source:HGNC Symbol;Acc:HGNC:21237] MITOCHONDRIAL COMPLEX III DEFICIENCY NUCLEAR TYPE 7
ENSG00000266509 MIR3934 microRNA 3934 [Source:HGNC Symbol;Acc:HGNC:38965]
ENSG00000161896 IP6K3 inositol hexakisphosphate kinase 3 [Source:HGNC Symbol;Acc:HGNC:17269]
ENSG00000161904 LEMD2 LEM domain containing 2 [Source:HGNC Symbol;Acc:HGNC:21244] Early-onset posterior subcapsular cataract
ENSG00000161904 LEMD2 LEM domain containing 2 [Source:HGNC Symbol;Acc:HGNC:21244] Total early-onset cataract
ENSG00000096395 MLN motilin [Source:HGNC Symbol;Acc:HGNC:7141]
ENSG00000249346 LINC01016 long intergenic non-protein coding RNA 1016 [Source:HGNC Symbol;Acc:HGNC:48991]
ENSG00000271362 AL138889.2
ENSG00000233183 AL138889.1
ENSG00000276824 MIR7159 microRNA 7159 [Source:HGNC Symbol;Acc:HGNC:49978]
ENSG00000221697 MIR1275 microRNA 1275 [Source:HGNC Symbol;Acc:HGNC:35346]
ENSG00000124493 GRM4 glutamate metabotropic receptor 4 [Source:HGNC Symbol;Acc:HGNC:4596]
ENSG00000271231 KRT18P9 keratin 18 pseudogene 9 [Source:HGNC Symbol;Acc:HGNC:17767]
ENSG00000214810 CYCSP55 cytochrome c, somatic pseudogene 55 [Source:HGNC Symbol;Acc:HGNC:21252]
ENSG00000137309 HMGA1 high mobility group AT-hook 1 [Source:HGNC Symbol;Acc:HGNC:5010] DIABETES MELLITUS NONINSULIN-DEPENDENT
ENSG00000276404 MIR6835 microRNA 6835 [Source:HGNC Symbol;Acc:HGNC:49963]
ENSG00000186577 SMIM29 small integral membrane protein 29 [Source:HGNC Symbol;Acc:HGNC:1340]
ENSG00000225339 AL354740.1
ENSG00000220583 RPL35P2 ribosomal protein L35 pseudogene 2 [Source:HGNC Symbol;Acc:HGNC:35789]
ENSG00000272325 NUDT3 nudix hydrolase 3 [Source:HGNC Symbol;Acc:HGNC:8050]
ENSG00000270800 RPS10-NUDT3 RPS10-NUDT3 readthrough [Source:HGNC Symbol;Acc:HGNC:49181]
ENSG00000124614 RPS10 ribosomal protein S10 [Source:HGNC Symbol;Acc:HGNC:10383] Blackfan-Diamond anemia
ENSG00000124614 RPS10 ribosomal protein S10 [Source:HGNC Symbol;Acc:HGNC:10383] DIAMOND-BLACKFAN ANEMIA 9
ENSG00000124507 PACSIN1 protein kinase C and casein kinase substrate in neurons 1 [Source:HGNC Symbol;Acc:HGNC:8570]
ENSG00000124664 SPDEF SAM pointed domain containing ETS transcription factor [Source:HGNC Symbol;Acc:HGNC:17257]
ENSG00000196114 AL031577.1
ENSG00000196821 C6orf106 chromosome 6 open reading frame 106 [Source:HGNC Symbol;Acc:HGNC:21215]
ENSG00000216636 RPL7P25 ribosomal protein L7 pseudogene 25 [Source:HGNC Symbol;Acc:HGNC:36455]
ENSG00000265123 RN7SL200P RNA, 7SL, cytoplasmic 200, pseudogene [Source:HGNC Symbol;Acc:HGNC:46216]
ENSG00000220643 AL031577.2
ENSG00000272288 AL451165.2
ENSG00000186328 AL451165.1
ENSG00000217130 AL139100.1
ENSG00000124562 SNRPC small nuclear ribonucleoprotein polypeptide C [Source:HGNC Symbol;Acc:HGNC:11157]
ENSG00000065060 UHRF1BP1 UHRF1 binding protein 1 [Source:HGNC Symbol;Acc:HGNC:21216]
ENSG00000206717 Y_RNA Y RNA [Source:RFAM;Acc:RF00019]
ENSG00000252106 RNY3P15 RNA, Ro-associated Y3 pseudogene 15 [Source:HGNC Symbol;Acc:HGNC:50890]
ENSG00000064995 TAF11 TATA-box binding protein associated factor 11 [Source:HGNC Symbol;Acc:HGNC:11544]
ENSG00000064999 ANKS1A ankyrin repeat and sterile alpha motif domain containing 1A [Source:HGNC Symbol;Acc:HGNC:20961]
# Or a even nicer table...
# library("DT")
# genes %>% datatable

Conclusion

See, now we know what is sitting in the region. Any guesses why did 23andMe put a lot of markers there?

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