Variant report

Variant	rs6888597
Chromosome Location	chr5:37598015-37598016
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	chr5:37595713..37598522-chr5:37598796..37602630,3	MCF-7	breast:

Extended variants
information (count: 181 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:164)

rs_ID	r²[population]
rs10037680	1.00[EUR][1000 genomes]
rs10038414	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10038482	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10039768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10042970	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10043213	1.00[EUR][1000 genomes]
rs10050392	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050932	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10051811	1.00[EUR][1000 genomes]
rs10053094	1.00[CEU][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055123	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055301	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055334	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055747	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10058062	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10059214	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10060693	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10063001	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10067239	1.00[EUR][1000 genomes]
rs10067278	1.00[CEU][hapmap]
rs10067869	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10070366	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10071032	1.00[CEU][hapmap]
rs10071967	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10072326	1.00[CEU][hapmap]
rs10074536	1.00[EUR][1000 genomes]
rs10075851	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10076872	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10077819	1.00[EUR][1000 genomes]
rs10078503	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10078741	1.00[CEU][hapmap]
rs10085007	1.00[EUR][1000 genomes]
rs10491332	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1104717	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1104718	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11739318	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11742290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11955258	1.00[EUR][1000 genomes]
rs12109225	1.00[EUR][1000 genomes]
rs12186464	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12332422	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332493	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12523118	1.00[EUR][1000 genomes]
rs12656455	1.00[EUR][1000 genomes]
rs13160250	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13166616	1.00[EUR][1000 genomes]
rs13175777	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13355660	1.00[EUR][1000 genomes]
rs13359981	1.00[EUR][1000 genomes]
rs1400855	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1554969	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16903615	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16903667	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16903675	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16903689	1.00[CEU][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903703	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16903704	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16903706	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16903711	1.00[CEU][hapmap]
rs1829294	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1973713	1.00[EUR][1000 genomes]
rs2056869	1.00[EUR][1000 genomes]
rs2142324	1.00[EUR][1000 genomes]
rs2366172	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2366175	1.00[EUR][1000 genomes]
rs28555070	1.00[EUR][1000 genomes]
rs28876205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34871356	1.00[EUR][1000 genomes]
rs4074950	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4242249	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4242250	1.00[EUR][1000 genomes]
rs4334908	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4370304	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4395662	1.00[EUR][1000 genomes]
rs4407651	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4407652	1.00[EUR][1000 genomes]
rs4418127	1.00[EUR][1000 genomes]
rs4449561	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4470784	1.00[EUR][1000 genomes]
rs4499858	1.00[EUR][1000 genomes]
rs4607372	1.00[EUR][1000 genomes]
rs475517	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs481834	1.00[EUR][1000 genomes]
rs4869431	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4869432	1.00[EUR][1000 genomes]
rs4869434	1.00[EUR][1000 genomes]
rs4869506	1.00[EUR][1000 genomes]
rs4869508	1.00[EUR][1000 genomes]
rs488315	1.00[EUR][1000 genomes]
rs489123	1.00[EUR][1000 genomes]
rs563999	1.00[EUR][1000 genomes]
rs587641	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs59176360	1.00[EUR][1000 genomes]
rs59468995	1.00[EUR][1000 genomes]
rs596461	1.00[EUR][1000 genomes]
rs60063938	1.00[EUR][1000 genomes]
rs61154857	1.00[EUR][1000 genomes]
rs61748201	1.00[EUR][1000 genomes]
rs626649	1.00[EUR][1000 genomes]
rs6451316	1.00[EUR][1000 genomes]
rs6451317	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6451318	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6451332	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs671077	1.00[EUR][1000 genomes]
rs6859972	1.00[EUR][1000 genomes]
rs6860757	1.00[EUR][1000 genomes]
rs6861640	1.00[CEU][hapmap]
rs6863124	1.00[EUR][1000 genomes]
rs6863547	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6868108	1.00[CEU][hapmap]
rs6868163	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6868843	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6869205	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6876447	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6892443	1.00[CEU][hapmap]
rs6895753	1.00[EUR][1000 genomes]
rs6898035	1.00[EUR][1000 genomes]
rs6898225	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6898271	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6898900	1.00[EUR][1000 genomes]
rs73068464	1.00[EUR][1000 genomes]
rs73068483	1.00[EUR][1000 genomes]
rs7702750	1.00[EUR][1000 genomes]
rs7702907	1.00[EUR][1000 genomes]
rs7703638	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7703670	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7704548	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7708301	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7708708	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709224	1.00[EUR][1000 genomes]
rs7710547	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714066	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7714241	1.00[EUR][1000 genomes]
rs7719190	1.00[EUR][1000 genomes]
rs7723389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7724308	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7724686	1.00[EUR][1000 genomes]
rs7725018	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7725049	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7725297	1.00[EUR][1000 genomes]
rs7727291	1.00[EUR][1000 genomes]
rs7727356	1.00[EUR][1000 genomes]
rs7727603	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7729195	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7729506	1.00[EUR][1000 genomes]
rs7732315	1.00[EUR][1000 genomes]
rs7732929	1.00[EUR][1000 genomes]
rs7733418	1.00[EUR][1000 genomes]
rs7734593	1.00[EUR][1000 genomes]
rs7735454	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7736469	1.00[EUR][1000 genomes]
rs7736605	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7736862	1.00[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7737210	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7737986	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8180378	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9292658	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292659	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292661	1.00[CEU][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292663	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs951579	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs971785	1.00[EUR][1000 genomes]
rs974432	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv1015983	chr5:37240827-37666601	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1021284	chr5:37264275-37630188	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1029088	chr5:37285576-37604945	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1034094	chr5:37406859-37666704	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv537731	chr5:37406859-37666704	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv880890	chr5:37443079-37681646	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv881497	chr5:37539060-37604856	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37540000-37621000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:37555000-37616200	Weak transcription	Aorta	Aorta
3	chr5:37572200-37620600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:37575600-37599600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:37575600-37611600	Weak transcription	Pancreas	Pancrea
6	chr5:37576000-37607800	Weak transcription	Left Ventricle	heart
7	chr5:37576600-37598800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:37587800-37601200	Weak transcription	Primary B cells from cord blood	blood
9	chr5:37588800-37628000	Weak transcription	Ovary	ovary
10	chr5:37590800-37599600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:37593400-37599800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr5:37593600-37600800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:37595600-37599400	Enhancers	Colon Smooth Muscle	Colon
14	chr5:37596800-37600800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:37597200-37599600	Weak transcription	Fetal Stomach	stomach
16	chr5:37597400-37600800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:37597800-37598800	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:37598000-37598200	Enhancers	Duodenum Smooth Muscle	Duodenum

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