Variant report

Variant	rs12708468
Chromosome Location	chr15:62162591-62162592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62160043..62163025-chr15:62359293..62361455,2	MCF-7	breast:

Extended variants
information (count: 121 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1000598	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1046156	0.88[CEU][hapmap]
rs10468027	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10519153	0.86[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs10851703	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10851704	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10851705	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11071634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071635	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11071636	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11071639	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11071641	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs11071647	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs11629528	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs11631013	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631970	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs11632774	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11632842	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11634516	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11634693	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11635621	0.82[ASN][1000 genomes]
rs11636504	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11638344	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438431	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439330	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12439934	0.86[YRI][hapmap]
rs12443311	0.82[EUR][1000 genomes]
rs12593844	0.83[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs12593860	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12595300	0.82[ASN][1000 genomes]
rs12708469	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12708470	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12898209	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12899801	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12901171	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901247	0.81[ASN][1000 genomes]
rs12901481	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12901575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12902092	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902409	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12908182	0.82[ASN][1000 genomes]
rs12909692	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12910541	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12912208	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1346036	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1364810	0.93[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1370177	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1436965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1436966	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1561197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17205225	0.86[EUR][1000 genomes]
rs17238252	0.85[CEU][hapmap];0.84[CHB][hapmap];0.96[JPT][hapmap]
rs17271151	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs17271158	0.83[AFR][1000 genomes]
rs17271235	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17303968	0.82[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap]
rs17304010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs1991205	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042608	0.83[YRI][hapmap]
rs2042610	0.93[CEU][hapmap];0.84[CHB][hapmap];0.96[JPT][hapmap];0.85[EUR][1000 genomes]
rs2059470	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2059471	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098850	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113932	0.89[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2113933	0.89[CEU][hapmap];0.84[CHB][hapmap];0.96[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2162064	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2216999	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2241491	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414754	0.82[CEU][hapmap]
rs2414756	0.82[ASN][1000 genomes]
rs28413840	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28472272	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28587331	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28591222	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28725250	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2899678	0.82[ASN][1000 genomes]
rs3210522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3743294	0.93[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3809517	1.00[CEU][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886246	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4372632	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4541010	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs4620905	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs4638519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs4774425	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4775442	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4775443	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4775444	0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4775445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4775447	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775448	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4775451	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6494299	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6494300	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs7161883	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7163326	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7163441	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164933	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168164	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172838	0.81[AMR][1000 genomes]
rs7402374	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023668	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs8025282	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028217	0.85[EUR][1000 genomes]
rs8029942	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs8033816	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs8034185	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs8035049	0.81[EUR][1000 genomes]
rs8037603	0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8038328	0.82[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs9788670	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9920945	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904284	chr15:62123600-62243197	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904285	chr15:62146598-62246864	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv904286	chr15:62146598-62313373	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv904287	chr15:62146598-62338797	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv904288	chr15:62146598-62356386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv569641	chr15:62155282-62287456	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv904289	chr15:62156690-62287456	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62132400-62171200	Weak transcription	HMEC	breast
2	chr15:62138800-62184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:62139200-62182200	Weak transcription	Brain Substantia Nigra	brain
4	chr15:62139800-62185200	Weak transcription	NHLF	lung
5	chr15:62140000-62184800	Weak transcription	Right Ventricle	heart
6	chr15:62140200-62180000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:62141200-62165400	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:62141600-62165000	Weak transcription	Thymus	Thymus
9	chr15:62142000-62165000	Weak transcription	Gastric	stomach
10	chr15:62142000-62209400	Weak transcription	Colonic Mucosa	Colon
11	chr15:62142200-62162800	Weak transcription	Hela-S3	cervix
12	chr15:62142400-62163800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:62142400-62253000	Weak transcription	Spleen	Spleen
14	chr15:62142600-62209200	Weak transcription	K562	blood
15	chr15:62143000-62164000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:62143800-62182200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:62143800-62235600	Weak transcription	Fetal Brain Male	brain
18	chr15:62144000-62194600	Weak transcription	Fetal Lung	lung
19	chr15:62144800-62184000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:62145200-62163400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:62145200-62182000	Weak transcription	NHEK	skin
22	chr15:62145400-62171600	Weak transcription	Stomach Mucosa	stomach
23	chr15:62145800-62182000	Weak transcription	Small Intestine	intestine
24	chr15:62146800-62230000	Weak transcription	Pancreas	Pancrea
25	chr15:62147000-62162800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:62147000-62181800	Weak transcription	Brain Anterior Caudate	brain
27	chr15:62147000-62184000	Weak transcription	Lung	lung
28	chr15:62147200-62164600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:62147200-62165200	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:62147400-62162600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:62147800-62184000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:62149000-62198000	Weak transcription	Fetal Kidney	kidney
33	chr15:62150000-62276200	Weak transcription	Psoas Muscle	Psoas
34	chr15:62150200-62165000	Weak transcription	Ovary	ovary
35	chr15:62150200-62165200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:62150200-62184200	Weak transcription	Aorta	Aorta
37	chr15:62150200-62185400	Weak transcription	Fetal Heart	heart
38	chr15:62150600-62162800	Weak transcription	HUVEC	blood vessel
39	chr15:62150600-62164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:62150800-62182000	Weak transcription	HSMMtube	muscle
41	chr15:62150800-62183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:62153200-62185400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:62153800-62185000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr15:62154200-62198200	Weak transcription	NH-A	brain
45	chr15:62154400-62184200	Weak transcription	Fetal Intestine Small	intestine
46	chr15:62154600-62183800	Weak transcription	Brain Angular Gyrus	brain
47	chr15:62154800-62184200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:62155000-62184600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:62155800-62162600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:62157200-62169000	Strong transcription	Primary T helper cells PMA-I stimulated	--

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