Variant report

Variant	rs12901171
Chromosome Location	chr15:62143442-62143443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:62142649..62144721-chr15:62150330..62151848,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1000598	0.85[EUR][1000 genomes]
rs10851703	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10851704	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10851705	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071634	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11071635	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11071636	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11071639	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631013	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631970	0.85[EUR][1000 genomes]
rs11632774	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634516	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11634693	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11636504	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638344	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438431	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439330	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12443311	0.83[EUR][1000 genomes]
rs12593860	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12708468	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708469	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708470	0.85[EUR][1000 genomes]
rs12901481	0.85[EUR][1000 genomes]
rs12902092	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12902409	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909692	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1346035	0.80[ASN][1000 genomes]
rs1346036	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1346037	0.80[ASN][1000 genomes]
rs1364810	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1370177	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17205225	0.85[EUR][1000 genomes]
rs17271151	0.85[EUR][1000 genomes]
rs17271158	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17271235	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17304010	0.83[ASN][1000 genomes]
rs1991205	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2042610	0.85[EUR][1000 genomes]
rs2059470	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2059471	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2098850	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2113932	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2113933	0.86[EUR][1000 genomes]
rs2162064	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2216999	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2241491	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28413840	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28472272	0.83[ASN][1000 genomes]
rs28587331	0.82[ASN][1000 genomes]
rs28591222	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28725250	0.83[ASN][1000 genomes]
rs3210522	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3743294	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3809517	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3886246	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4541010	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4774425	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4775442	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4775443	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4775444	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4775445	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4775447	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4775448	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4775451	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494299	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7163441	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164933	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7168164	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7172838	0.81[AMR][1000 genomes]
rs7402374	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8025282	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8028217	0.86[EUR][1000 genomes]
rs8034185	0.85[EUR][1000 genomes]
rs8035049	0.82[EUR][1000 genomes]
rs8037603	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8038328	0.81[AMR][1000 genomes]
rs9788670	0.81[EUR][1000 genomes]
rs9920945	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62132400-62159000	Weak transcription	HSMM	muscle
2	chr15:62132400-62171200	Weak transcription	HMEC	breast
3	chr15:62132800-62146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:62134000-62144200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:62135000-62161600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:62136800-62150000	Weak transcription	HSMMtube	muscle
7	chr15:62137200-62144800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:62137400-62145400	Weak transcription	Liver	Liver
9	chr15:62138800-62184200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:62139200-62144000	Weak transcription	Lung	lung
11	chr15:62139200-62146000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:62139200-62146600	Weak transcription	Pancreas	Pancrea
13	chr15:62139200-62182200	Weak transcription	Brain Substantia Nigra	brain
14	chr15:62139400-62154800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:62139600-62143600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:62139600-62145400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:62139800-62185200	Weak transcription	NHLF	lung
18	chr15:62140000-62144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:62140000-62184800	Weak transcription	Right Ventricle	heart
20	chr15:62140200-62180000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:62140400-62145800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:62140800-62143800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr15:62140800-62146400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:62140800-62149000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:62141000-62144000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:62141000-62149400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:62141200-62149600	Weak transcription	Psoas Muscle	Psoas
28	chr15:62141200-62165400	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:62141400-62144000	Weak transcription	Dnd41	blood
30	chr15:62141400-62146600	Weak transcription	GM12878-XiMat	blood
31	chr15:62141400-62160600	Weak transcription	Placenta	Placenta
32	chr15:62141400-62161400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:62141600-62146200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:62141600-62146400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:62141600-62149200	Weak transcription	Ovary	ovary
36	chr15:62141600-62161400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:62141600-62165000	Weak transcription	Thymus	Thymus
38	chr15:62141800-62145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:62141800-62146400	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:62141800-62149400	Weak transcription	Aorta	Aorta
41	chr15:62142000-62145600	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:62142000-62147400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:62142000-62165000	Weak transcription	Gastric	stomach
44	chr15:62142000-62209400	Weak transcription	Colonic Mucosa	Colon
45	chr15:62142200-62161600	Weak transcription	Fetal Stomach	stomach
46	chr15:62142200-62162800	Weak transcription	Hela-S3	cervix
47	chr15:62142400-62144600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr15:62142400-62146400	Weak transcription	Brain Anterior Caudate	brain
49	chr15:62142400-62160800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr15:62142400-62163800	Weak transcription	Brain Inferior Temporal Lobe	brain

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