Variant report

Variant	rs3804231
Chromosome Location	chr5:74696779-74696780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:74696648-74696833	K562	blood:	n/a	n/a

Variant related genes	Relation type
COL4A3BP	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10036682	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10038945	0.89[EUR][1000 genomes]
rs10041470	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10055011	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10059022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10061689	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10067900	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10076819	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10077427	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs10078671	0.89[EUR][1000 genomes]
rs10474437	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12173076	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13360099	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13361353	0.93[EUR][1000 genomes]
rs1422702	0.85[CEU][hapmap]
rs1469051	0.85[EUR][1000 genomes]
rs1553234	0.93[EUR][1000 genomes]
rs1820049	0.88[EUR][1000 genomes]
rs1909719	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2287710	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28408106	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28612248	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28668361	0.89[EUR][1000 genomes]
rs28874007	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703671	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703675	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4704213	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704229	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56859362	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5744544	0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs5744545	0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs5744636	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5744667	0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs5744704	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs5744709	0.88[EUR][1000 genomes]
rs5744712	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs57907925	0.85[EUR][1000 genomes]
rs58519566	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58841453	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61303403	0.81[EUR][1000 genomes]
rs6891560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633963	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72633964	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72633965	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72633966	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72633967	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72633968	0.90[EUR][1000 genomes]
rs72633969	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633970	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633971	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72633972	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72633973	0.93[EUR][1000 genomes]
rs72633974	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72633975	0.89[EUR][1000 genomes]
rs72633976	0.87[EUR][1000 genomes]
rs72633977	0.81[EUR][1000 genomes]
rs7356633	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726478	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs904743	0.85[EUR][1000 genomes]
rs9293652	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9293654	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9293655	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs979182	0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882192	chr5:74641707-74707762	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3804231	ARSB	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74656400-74725600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:74656800-74731400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:74657800-74708000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:74659800-74720600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:74660000-74722800	Weak transcription	Fetal Heart	heart
6	chr5:74660200-74707800	Weak transcription	Stomach Mucosa	stomach
7	chr5:74665000-74703000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:74667000-74723200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:74670800-74709400	Weak transcription	Pancreas	Pancrea
10	chr5:74670800-74720600	Weak transcription	Right Ventricle	heart
11	chr5:74670800-74731400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:74671000-74722800	Weak transcription	Hela-S3	cervix
13	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
14	chr5:74675400-74699600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:74675400-74720800	Weak transcription	Small Intestine	intestine
16	chr5:74676200-74721000	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:74677000-74701000	Weak transcription	A549	lung
18	chr5:74677400-74722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:74677600-74709200	Weak transcription	Gastric	stomach
20	chr5:74677600-74734200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:74677800-74721000	Weak transcription	NH-A	brain
22	chr5:74677800-74725000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:74677800-74731400	Weak transcription	Aorta	Aorta
24	chr5:74678000-74708000	Weak transcription	NHLF	lung
25	chr5:74678000-74720600	Weak transcription	Colonic Mucosa	Colon
26	chr5:74678000-74730800	Weak transcription	Psoas Muscle	Psoas
27	chr5:74680600-74721000	Weak transcription	HMEC	breast
28	chr5:74680800-74722600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:74681000-74723200	Weak transcription	HUVEC	blood vessel
30	chr5:74681400-74718400	Weak transcription	Brain Germinal Matrix	brain
31	chr5:74681800-74720600	Weak transcription	Fetal Brain Male	brain
32	chr5:74682000-74699000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:74682000-74708000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr5:74682200-74705000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:74683200-74698600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:74684000-74704200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:74684000-74709000	Weak transcription	Spleen	Spleen
38	chr5:74684000-74720400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:74684000-74720800	Weak transcription	Thymus	Thymus
40	chr5:74684000-74731200	Weak transcription	HSMMtube	muscle
41	chr5:74684800-74705400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:74684800-74705400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:74685200-74707200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:74685200-74708400	Weak transcription	Osteobl	bone
45	chr5:74685600-74699000	Weak transcription	NHDF-Ad	bronchial
46	chr5:74685800-74697800	Weak transcription	GM12878-XiMat	blood
47	chr5:74685800-74709200	Weak transcription	Dnd41	blood
48	chr5:74685800-74711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:74686000-74707800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:74689000-74699600	Strong transcription	Primary neutrophils fromperipheralblood	blood

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