Variant report

Variant	rs4838429
Chromosome Location	chr10:49841549-49841550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10776629	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10776630	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10776631	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10776632	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10857612	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10857613	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857614	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1822861	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2377522	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2377523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2377595	0.87[ASW][hapmap];0.82[CHB][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2377596	0.82[EUR][1000 genomes]
rs34939981	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3844493	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3845284	0.84[EUR][1000 genomes]
rs3853123	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3910909	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3910910	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3910911	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3910912	0.81[JPT][hapmap];0.92[MEX][hapmap]
rs4562728	0.81[MKK][hapmap];0.80[AFR][1000 genomes]
rs4838428	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7904633	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4838429	ARHGAP22	cis	Artery Aorta	GTEx
rs4838429	ARHGAP22	cis	Artery Tibial	GTEx
rs4838429	ARHGAP22	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49813400-49844200	Weak transcription	Pancreas	Pancrea
2	chr10:49831600-49843400	Weak transcription	Right Atrium	heart
3	chr10:49832400-49842000	Weak transcription	Brain Substantia Nigra	brain
4	chr10:49834200-49842000	Weak transcription	NHLF	lung
5	chr10:49837400-49841600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:49839600-49842000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:49839800-49842000	Enhancers	Osteobl	bone
8	chr10:49839800-49842200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr10:49840000-49842000	Enhancers	HSMM	muscle
10	chr10:49840000-49842200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr10:49840000-49842600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:49840000-49842800	Enhancers	HSMMtube	muscle
13	chr10:49840200-49848600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr10:49840400-49842000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:49840400-49842000	Enhancers	GM12878-XiMat	blood
16	chr10:49840400-49845000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr10:49840600-49841600	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr10:49840800-49844000	Enhancers	Primary hematopoietic stem cells	blood
19	chr10:49840800-49844400	Enhancers	NHDF-Ad	bronchial
20	chr10:49841000-49842400	Enhancers	Colonic Mucosa	Colon
21	chr10:49841000-49843200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr10:49841000-49843400	Enhancers	Primary B cells from peripheral blood	blood
23	chr10:49841000-49843800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:49841000-49844000	Enhancers	Dnd41	blood
25	chr10:49841000-49845200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:49841200-49842400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr10:49841200-49843200	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr10:49841400-49841800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:49841400-49842200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:49841400-49843000	Enhancers	Primary B cells from cord blood	blood
31	chr10:49841400-49843400	Enhancers	Aorta	Aorta

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