Variant report

Variant	rs1812936
Chromosome Location	chr5:49720191-49720192
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49713946..49715979-chr5:49717619..49720467,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10042504	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10042601	0.81[EUR][1000 genomes]
rs10043101	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10051529	0.80[EUR][1000 genomes]
rs10061339	0.88[EUR][1000 genomes]
rs10062032	0.81[EUR][1000 genomes]
rs10071725	0.87[EUR][1000 genomes]
rs10072182	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10073530	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10074359	0.81[EUR][1000 genomes]
rs10076490	0.81[ASN][1000 genomes]
rs10079493	0.86[EUR][1000 genomes]
rs1010676	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]
rs1016621	0.81[EUR][1000 genomes]
rs1039798	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10940334	0.83[EUR][1000 genomes]
rs10940335	0.83[EUR][1000 genomes]
rs10940336	0.83[EUR][1000 genomes]
rs11948302	0.83[EUR][1000 genomes]
rs11959569	0.87[EUR][1000 genomes]
rs12109228	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12659303	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12697055	0.81[EUR][1000 genomes]
rs13153021	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13157992	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs13173678	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs13174293	0.85[EUR][1000 genomes]
rs13180579	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13180767	0.85[EUR][1000 genomes]
rs13180852	0.88[EUR][1000 genomes]
rs13182357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13184466	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13184498	0.82[EUR][1000 genomes]
rs13184661	0.83[EUR][1000 genomes]
rs13357429	0.90[CEU][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1344339	0.82[EUR][1000 genomes]
rs1606224	0.81[EUR][1000 genomes]
rs16879094	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1811742	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1833900	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1967289	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036901	0.89[JPT][hapmap]
rs2036902	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2137134	0.85[EUR][1000 genomes]
rs2271236	0.80[JPT][hapmap]
rs2668024	0.90[JPT][hapmap]
rs28445612	0.90[JPT][hapmap]
rs28500170	0.91[EUR][1000 genomes]
rs28528780	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28676351	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2883164	0.81[JPT][hapmap]
rs303219	0.81[JPT][hapmap]
rs34044048	0.89[EUR][1000 genomes]
rs34185098	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34433187	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34601168	0.81[EUR][1000 genomes]
rs34741488	0.89[EUR][1000 genomes]
rs34749302	0.83[EUR][1000 genomes]
rs34774804	0.85[EUR][1000 genomes]
rs34945845	0.95[EUR][1000 genomes]
rs34950042	0.88[EUR][1000 genomes]
rs35740733	0.83[EUR][1000 genomes]
rs35858778	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35866059	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849669	0.87[EUR][1000 genomes]
rs3860731	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3860732	0.87[EUR][1000 genomes]
rs3933097	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4029989	0.87[EUR][1000 genomes]
rs4030571	0.87[EUR][1000 genomes]
rs4031137	0.89[EUR][1000 genomes]
rs4145844	0.88[EUR][1000 genomes]
rs4277861	0.84[EUR][1000 genomes]
rs4337857	0.83[EUR][1000 genomes]
rs4398636	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4495185	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4637546	0.85[EUR][1000 genomes]
rs57137858	0.87[EUR][1000 genomes]
rs57583601	0.89[EUR][1000 genomes]
rs58756661	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59254474	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62365896	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62365901	0.91[EUR][1000 genomes]
rs62365902	0.85[EUR][1000 genomes]
rs62386175	0.89[EUR][1000 genomes]
rs6450056	0.85[EUR][1000 genomes]
rs6450063	0.89[EUR][1000 genomes]
rs6450098	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6450099	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450107	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6450139	0.87[EUR][1000 genomes]
rs6860503	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6863840	0.82[EUR][1000 genomes]
rs6868380	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6868677	0.86[EUR][1000 genomes]
rs6868721	1.00[CEU][hapmap]
rs6871761	0.82[EUR][1000 genomes]
rs6876902	0.81[EUR][1000 genomes]
rs6877713	0.82[EUR][1000 genomes]
rs6897412	0.83[EUR][1000 genomes]
rs7341010	0.81[EUR][1000 genomes]
rs7442762	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7446951	0.81[EUR][1000 genomes]
rs7706105	0.83[EUR][1000 genomes]
rs7712849	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7717982	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7719081	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7722742	0.81[EUR][1000 genomes]
rs7732000	0.84[EUR][1000 genomes]
rs9291925	0.81[EUR][1000 genomes]
rs9292005	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9716734	0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1812936	EMB	cis	Whole Blood	GTEx
rs1812936	EMB	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:49697400-49723400	Weak transcription	HSMM	muscle
4	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:49713000-49722000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:49713000-49722600	Weak transcription	Fetal Thymus	thymus
9	chr5:49713000-49725800	Weak transcription	Small Intestine	intestine
10	chr5:49714800-49721200	Weak transcription	Primary T cells from cord blood	blood
11	chr5:49715000-49722600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:49715000-49723400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr5:49715000-49723800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:49716600-49720400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr5:49716600-49722000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr5:49716800-49720200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:49717000-49723600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:49717200-49722000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:49717800-49723800	Strong transcription	Dnd41	blood
20	chr5:49718200-49720400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:49718200-49721800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:49718400-49727400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:49718600-49721400	Weak transcription	Primary B cells from cord blood	blood
24	chr5:49719000-49720200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:49719000-49720400	Enhancers	HMEC	breast
26	chr5:49719000-49720600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:49719000-49720600	Enhancers	NHEK	skin
28	chr5:49719000-49722800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:49719200-49720200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:49719200-49720400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:49719200-49721400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:49719200-49726800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:49719400-49723600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:49719600-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:49719600-49723800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:49719800-49724000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:49720000-49720400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:49720000-49723600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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