Variant report

Variant	rs3860731
Chromosome Location	chr5:49697863-49697864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10041903	0.82[EUR][1000 genomes]
rs10042504	0.93[EUR][1000 genomes]
rs10042601	0.85[EUR][1000 genomes]
rs10043101	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10051529	0.85[EUR][1000 genomes]
rs10056605	0.83[EUR][1000 genomes]
rs10062032	0.85[EUR][1000 genomes]
rs10071725	0.92[EUR][1000 genomes]
rs10072182	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10073530	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10074359	0.85[EUR][1000 genomes]
rs10079493	0.92[EUR][1000 genomes]
rs1010676	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1039798	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10461390	0.82[EUR][1000 genomes]
rs10461391	0.83[EUR][1000 genomes]
rs11959569	0.92[EUR][1000 genomes]
rs12109228	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12188175	0.82[EUR][1000 genomes]
rs12513730	0.84[EUR][1000 genomes]
rs12659303	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12697055	0.85[EUR][1000 genomes]
rs13153021	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13157992	0.80[EUR][1000 genomes]
rs13174293	0.90[EUR][1000 genomes]
rs13180579	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13180767	0.93[EUR][1000 genomes]
rs13182357	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13184466	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13357429	0.89[EUR][1000 genomes]
rs1344339	0.86[EUR][1000 genomes]
rs1511737	0.84[EUR][1000 genomes]
rs1511738	0.84[EUR][1000 genomes]
rs1606224	0.85[EUR][1000 genomes]
rs16879094	0.80[EUR][1000 genomes]
rs1811742	0.81[EUR][1000 genomes]
rs1812936	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1967289	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2005573	0.84[EUR][1000 genomes]
rs2011539	0.83[EUR][1000 genomes]
rs2011540	0.83[EUR][1000 genomes]
rs2036902	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2137129	0.84[EUR][1000 genomes]
rs2137134	0.90[EUR][1000 genomes]
rs28500170	0.80[EUR][1000 genomes]
rs28528780	0.80[EUR][1000 genomes]
rs34185098	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34433187	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34601168	0.86[EUR][1000 genomes]
rs34741488	0.93[EUR][1000 genomes]
rs34749302	0.90[EUR][1000 genomes]
rs34945845	0.90[EUR][1000 genomes]
rs35740733	0.87[EUR][1000 genomes]
rs35858778	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35866059	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3849669	0.92[EUR][1000 genomes]
rs3860732	0.92[EUR][1000 genomes]
rs3933097	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4030571	0.92[EUR][1000 genomes]
rs4031137	0.93[EUR][1000 genomes]
rs4337857	0.87[EUR][1000 genomes]
rs4398636	0.93[EUR][1000 genomes]
rs4495185	0.89[EUR][1000 genomes]
rs4605784	0.83[EUR][1000 genomes]
rs4637546	0.90[EUR][1000 genomes]
rs471455	0.80[EUR][1000 genomes]
rs4865519	0.84[EUR][1000 genomes]
rs4865698	0.84[EUR][1000 genomes]
rs4865699	0.84[EUR][1000 genomes]
rs4865700	0.84[EUR][1000 genomes]
rs494540	0.80[EUR][1000 genomes]
rs5011669	0.84[EUR][1000 genomes]
rs552892	0.81[EUR][1000 genomes]
rs57137858	0.92[EUR][1000 genomes]
rs58178891	0.82[EUR][1000 genomes]
rs58756661	0.81[EUR][1000 genomes]
rs62365896	0.88[EUR][1000 genomes]
rs62386175	0.93[EUR][1000 genomes]
rs6449961	0.84[EUR][1000 genomes]
rs6450056	0.89[EUR][1000 genomes]
rs6450063	0.93[EUR][1000 genomes]
rs6450098	0.88[EUR][1000 genomes]
rs6450099	0.85[EUR][1000 genomes]
rs6450107	0.81[EUR][1000 genomes]
rs6860503	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863840	0.86[EUR][1000 genomes]
rs6868380	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6868677	0.95[EUR][1000 genomes]
rs6871761	0.86[EUR][1000 genomes]
rs6876902	0.85[EUR][1000 genomes]
rs6877713	0.86[EUR][1000 genomes]
rs6897412	0.87[EUR][1000 genomes]
rs7341010	0.85[EUR][1000 genomes]
rs7442762	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7446951	0.85[EUR][1000 genomes]
rs7447926	0.84[EUR][1000 genomes]
rs7712849	0.91[EUR][1000 genomes]
rs7717982	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7722742	0.85[EUR][1000 genomes]
rs7732000	0.87[EUR][1000 genomes]
rs9291925	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3860731	EMB	cis	Whole Blood	GTEx
rs3860731	EMB	cis	Skin Sun Exposed Lower leg	GTEx
rs3860731	EMB	cis	Thyroid	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49682000-49719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:49685000-49700800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:49688800-49707200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:49688800-49710000	Weak transcription	Fetal Thymus	thymus
5	chr5:49689400-49701400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:49690000-49701000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:49690000-49701400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:49690400-49708600	Strong transcription	Dnd41	blood
10	chr5:49690600-49706800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:49690800-49702600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:49691000-49702400	Weak transcription	NHEK	skin
13	chr5:49691000-49702600	Weak transcription	HMEC	breast
14	chr5:49692400-49698200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:49692800-49708000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:49693000-49707600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:49693400-49707000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:49693800-49699400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:49694200-49707000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:49694400-49702600	Weak transcription	Fetal Intestine Large	intestine
21	chr5:49694600-49706400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:49695200-49705800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:49695400-49699000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:49695400-49701000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr5:49695600-49699000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:49695600-49699200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:49695600-49708400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:49695800-49698200	Strong transcription	Primary hematopoietic stem cells	blood
29	chr5:49696000-49699200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr5:49696200-49701000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr5:49696400-49698000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:49696600-49701000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:49696800-49698400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:49697200-49699200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:49697400-49702600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:49697400-49723400	Weak transcription	HSMM	muscle
38	chr5:49697600-49699000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:49697600-49702400	Weak transcription	Primary B cells from cord blood	blood
40	chr5:49697600-49709800	Weak transcription	Primary T cells from cord blood	blood
41	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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