Variant report

Variant	rs1010676
Chromosome Location	chr5:49709068-49709069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10042504	0.87[EUR][1000 genomes]
rs10043101	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10061339	0.84[EUR][1000 genomes]
rs10071725	0.86[EUR][1000 genomes]
rs10072182	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10073530	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10079493	0.86[EUR][1000 genomes]
rs1039798	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11959569	0.86[EUR][1000 genomes]
rs12109228	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12659303	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13153021	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13157992	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs13173678	0.90[JPT][hapmap]
rs13174293	0.84[EUR][1000 genomes]
rs13180579	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13180767	0.87[EUR][1000 genomes]
rs13180852	0.84[EUR][1000 genomes]
rs13182357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13184466	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13357429	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs1344339	0.81[EUR][1000 genomes]
rs16879094	0.87[EUR][1000 genomes]
rs1811742	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1812936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1833900	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1967289	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2036901	0.89[JPT][hapmap]
rs2036902	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2137134	0.84[EUR][1000 genomes]
rs2271236	0.89[JPT][hapmap]
rs2668024	0.90[JPT][hapmap]
rs28445612	0.90[JPT][hapmap]
rs28500170	0.87[EUR][1000 genomes]
rs28528780	0.87[EUR][1000 genomes]
rs28676351	0.85[EUR][1000 genomes]
rs2883164	0.89[JPT][hapmap]
rs303219	0.90[JPT][hapmap]
rs34044048	0.85[EUR][1000 genomes]
rs34185098	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34433187	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34601168	0.80[EUR][1000 genomes]
rs34741488	0.87[EUR][1000 genomes]
rs34749302	0.83[EUR][1000 genomes]
rs34774804	0.81[EUR][1000 genomes]
rs34945845	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34950042	0.84[EUR][1000 genomes]
rs35740733	0.82[EUR][1000 genomes]
rs35858778	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35866059	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3849669	0.86[EUR][1000 genomes]
rs3860731	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3860732	0.86[EUR][1000 genomes]
rs3933097	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4029989	0.83[EUR][1000 genomes]
rs4030571	0.86[EUR][1000 genomes]
rs4031137	0.87[EUR][1000 genomes]
rs4145844	0.84[EUR][1000 genomes]
rs4277861	0.80[EUR][1000 genomes]
rs4337857	0.82[EUR][1000 genomes]
rs4398636	0.87[EUR][1000 genomes]
rs4495185	0.96[EUR][1000 genomes]
rs4637546	0.84[EUR][1000 genomes]
rs57137858	0.86[EUR][1000 genomes]
rs57583601	0.85[EUR][1000 genomes]
rs58756661	0.87[EUR][1000 genomes]
rs59254474	0.86[EUR][1000 genomes]
rs62365896	0.95[EUR][1000 genomes]
rs62365901	0.86[EUR][1000 genomes]
rs62365902	0.81[EUR][1000 genomes]
rs62386175	0.87[EUR][1000 genomes]
rs6450056	0.84[EUR][1000 genomes]
rs6450063	0.87[EUR][1000 genomes]
rs6450098	0.95[EUR][1000 genomes]
rs6450099	0.92[EUR][1000 genomes]
rs6450107	0.87[EUR][1000 genomes]
rs6450139	0.83[EUR][1000 genomes]
rs6860503	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863840	0.81[EUR][1000 genomes]
rs6868380	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6868677	0.89[EUR][1000 genomes]
rs6868721	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap]
rs6871761	0.81[EUR][1000 genomes]
rs6877713	0.81[EUR][1000 genomes]
rs6897412	0.82[EUR][1000 genomes]
rs7442762	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7712849	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs7717982	0.90[EUR][1000 genomes]
rs7719081	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7732000	0.82[EUR][1000 genomes]
rs9292005	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs9716734	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1010676	EMB	cis	parietal	SCAN
rs1010676	ARL15	cis	parietal	SCAN
rs1010676	EMB	cis	Skin Sun Exposed Lower leg	GTEx
rs1010676	EMB	cis	Thyroid	GTEx
rs1010676	LOC647121	trans	multi-tissue	Pritchard
rs1010676	EMB	cis	Whole Blood	GTEx

Chromatin state (count:35 , 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	chr5:49688800-49710000	Weak transcription	Fetal Thymus	thymus
3	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:49697400-49723400	Weak transcription	HSMM	muscle
6	chr5:49697600-49709800	Weak transcription	Primary T cells from cord blood	blood
7	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:49698200-49711600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:49701000-49711400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:49703200-49709200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:49703200-49719000	Weak transcription	HMEC	breast
13	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:49703400-49711800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr5:49703600-49711400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:49704200-49710000	Weak transcription	Fetal Intestine Small	intestine
18	chr5:49704400-49711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:49705200-49709200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:49705200-49710600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr5:49705400-49709400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr5:49705400-49715800	Weak transcription	Fetal Intestine Large	intestine
23	chr5:49705600-49709800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:49706200-49709800	Weak transcription	Primary B cells from cord blood	blood
25	chr5:49706800-49710000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:49707200-49715000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr5:49707600-49709800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:49708200-49710000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:49708600-49709800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:49708600-49709800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:49708600-49710000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:49708600-49710000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:49708600-49711000	Weak transcription	Dnd41	blood
34	chr5:49708800-49710000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:49709000-49709400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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