Variant report

Variant	rs17706179
Chromosome Location	chr15:39915163-39915164
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:39911219..39913428-chr15:39914753..39916393,2	MCF-7	breast:
2	chr15:39889048..39893948-chr15:39913567..39917542,6	MCF-7	breast:
3	chr15:39872530..39878181-chr15:39914348..39917855,8	MCF-7	breast:
4	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
5	chr15:39913257..39915951-chr15:39916082..39918090,3	K562	blood:
6	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
7	chr15:39872636..39875230-chr15:39915122..39916947,2	MCF-7	breast:
8	chr15:39913193..39915951-chr15:39916034..39918090,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10152903	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10152951	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1038097	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10520143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10520146	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap]
rs1073675	1.00[CHB][hapmap]
rs12438058	1.00[ASN][1000 genomes]
rs12442155	1.00[ASN][1000 genomes]
rs12442221	1.00[ASN][1000 genomes]
rs1382443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969143	1.00[ASN][1000 genomes]
rs16969167	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16969487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16969491	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16969547	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs16969663	1.00[CHB][hapmap]
rs16969664	1.00[CHB][hapmap]
rs16969666	1.00[CHB][hapmap]
rs16969672	1.00[CHB][hapmap]
rs16969679	1.00[CHB][hapmap]
rs16969680	1.00[CHB][hapmap]
rs16969688	1.00[CHB][hapmap]
rs17631807	1.00[ASN][1000 genomes]
rs17632916	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17633107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702987	1.00[ASN][1000 genomes]
rs17705806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17717859	1.00[CHB][hapmap]
rs1813493	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988082	0.80[EUR][1000 genomes]
rs1988555	0.84[EUR][1000 genomes]
rs1994380	1.00[CHB][hapmap]
rs2129457	1.00[CHB][hapmap]
rs2228262	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2228263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2618156	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618160	0.91[EUR][1000 genomes]
rs2618161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618164	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2618165	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2618166	1.00[ASN][1000 genomes]
rs2618167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664123	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664136	0.90[EUR][1000 genomes]
rs2664137	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs2664140	0.91[EUR][1000 genomes]
rs2664142	0.91[EUR][1000 genomes]
rs28377784	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28549326	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28619289	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28622135	1.00[ASN][1000 genomes]
rs28653011	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34878675	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35275624	1.00[ASN][1000 genomes]
rs41315060	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4503768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45461294	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4923835	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58188999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59578395	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59628570	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62002368	1.00[ASN][1000 genomes]
rs62002377	1.00[ASN][1000 genomes]
rs62002378	1.00[ASN][1000 genomes]
rs62002379	1.00[ASN][1000 genomes]
rs62002380	1.00[ASN][1000 genomes]
rs62002384	1.00[ASN][1000 genomes]
rs6492905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7172155	1.00[CHB][hapmap]
rs7173948	1.00[CHB][hapmap]
rs7179604	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7181354	1.00[CHB][hapmap]
rs7182423	1.00[CHB][hapmap]
rs74008526	1.00[ASN][1000 genomes]
rs74008647	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008648	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8041266	1.00[CHB][hapmap]
rs880270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs937961	1.00[CHB][hapmap]
rs937962	1.00[CHB][hapmap]
rs954152	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9972350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39906600-39916000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:39910600-39915400	Weak transcription	A549	lung
3	chr15:39910800-39916200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:39910800-39917400	Weak transcription	Small Intestine	intestine
5	chr15:39911000-39916000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:39911000-39916200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:39911000-39916200	Weak transcription	Left Ventricle	heart
8	chr15:39911000-39916400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:39911400-39916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:39912000-39916000	Weak transcription	HMEC	breast
11	chr15:39912800-39916000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:39913200-39924000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr15:39913400-39915200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:39913400-39915400	Enhancers	Colon Smooth Muscle	Colon
15	chr15:39913400-39918200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:39913400-39921000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:39913400-39922400	Enhancers	Fetal Intestine Large	intestine
18	chr15:39913400-39923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:39913600-39916000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:39913800-39915800	Weak transcription	HUVEC	blood vessel
21	chr15:39913800-39916400	Weak transcription	NHEK	skin
22	chr15:39913800-39916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:39913800-39917200	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:39914000-39922800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:39914200-39916000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:39914200-39916600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:39914200-39922600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr15:39914600-39915200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr15:39914600-39922800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr15:39914600-39923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:39914600-39923600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr15:39914600-39923800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr15:39914800-39915400	Enhancers	GM12878-XiMat	blood
34	chr15:39914800-39916200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:39914800-39916600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:39914800-39923800	Enhancers	Primary T cells fromperipheralblood	blood
37	chr15:39915000-39915200	Enhancers	Stomach Mucosa	stomach
38	chr15:39915000-39916000	Enhancers	Rectal Mucosa Donor 29	rectum

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