Variant report

Variant	rs7954119
Chromosome Location	chr12:82866639-82866640
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	chr12:82864287..82866811-chr3:130394292..130397010,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10219540	0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10732677	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10735454	0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10735455	0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10746243	0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10746247	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10746248	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10746250	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10746251	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10778894	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10778897	0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10778903	0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10778904	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10778905	0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10778906	0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10778908	0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10862481	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10862484	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10862485	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10862486	0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11837949	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17009470	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17009622	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009629	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17719033	0.94[EUR][1000 genomes]
rs17775000	0.94[EUR][1000 genomes]
rs17775447	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17775501	0.94[EUR][1000 genomes]
rs17776114	0.89[EUR][1000 genomes]
rs1874058	0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254688	0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs2401026	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2401027	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2401032	0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2401039	0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642015	0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642017	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642018	0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642019	0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642021	0.88[EUR][1000 genomes]
rs2642023	0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2717449	0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs2717459	0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731286	0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731288	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731289	0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2731290	0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731291	0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731292	0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731294	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2731295	0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731297	0.91[EUR][1000 genomes]
rs28626834	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2895910	0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2895911	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2895912	0.83[YRI][hapmap];0.88[EUR][1000 genomes]
rs2895915	0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4143187	0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41535250	1.00[EUR][1000 genomes]
rs4242864	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4257045	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4284465	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4296098	0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4334093	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4343090	0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4356298	0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4370996	0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4387422	0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4399377	0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4417379	0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4460874	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4495950	1.00[JPT][hapmap]
rs4505128	0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4516038	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4517594	0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4540892	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4553425	0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4587790	0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4628747	0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4882379	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4882386	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4882389	0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4882390	0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4882435	0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4882438	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4882541	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4882542	0.82[EUR][1000 genomes]
rs55806388	1.00[EUR][1000 genomes]
rs55887136	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56337649	0.94[EUR][1000 genomes]
rs6539669	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7133956	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7294771	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7294903	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7297164	0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7299307	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7299616	0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7309442	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7313975	0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7316500	0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7953161	0.89[EUR][1000 genomes]
rs7953234	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7954460	0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7968677	0.88[AMR][1000 genomes]
rs7969953	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7971746	0.87[AFR][1000 genomes]
rs7977443	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8181688	0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8181705	0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][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	nsv559539	chr12:82280797-82896218	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
2	nsv1041954	chr12:82314981-83008609	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv541550	chr12:82314981-83008609	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases
4	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv1841396	chr12:82768717-82881082	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv519197	chr12:82831845-83056476	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82804600-82869400	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:82823200-82868000	Weak transcription	Brain Angular Gyrus	brain
3	chr12:82824200-82868200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:82832200-82869600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:82832400-82873400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:82832600-82869800	Weak transcription	Gastric	stomach
7	chr12:82833000-82866800	Weak transcription	Lung	lung
8	chr12:82833400-82866800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:82834000-82874400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:82834200-82866800	Weak transcription	Esophagus	oesophagus
11	chr12:82834200-82866800	Weak transcription	Spleen	Spleen
12	chr12:82834600-82868200	Weak transcription	Colonic Mucosa	Colon
13	chr12:82836400-82868400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:82836400-82870000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:82837000-82868000	Weak transcription	Fetal Heart	heart
16	chr12:82837800-82876400	Weak transcription	Psoas Muscle	Psoas
17	chr12:82849800-82868600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:82853000-82869200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:82853800-82866800	Weak transcription	Fetal Stomach	stomach
20	chr12:82854000-82866800	Weak transcription	Aorta	Aorta
21	chr12:82854000-82866800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:82854000-82868400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:82854200-82866800	Weak transcription	Fetal Intestine Large	intestine
24	chr12:82856200-82868000	Weak transcription	HMEC	breast
25	chr12:82859600-82868000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:82861400-82867200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:82862800-82869600	Weak transcription	Pancreas	Pancrea
28	chr12:82862800-82873000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:82863000-82866800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:82863000-82867400	Weak transcription	Liver	Liver
31	chr12:82863000-82868800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:82863200-82866800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:82863200-82867600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:82863200-82868000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:82863200-82868400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:82863400-82866800	Weak transcription	Primary B cells from cord blood	blood
37	chr12:82863400-82866800	Weak transcription	Adipose Nuclei	Adipose
38	chr12:82863400-82866800	Weak transcription	Ovary	ovary
39	chr12:82864000-82868400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:82864600-82868000	Weak transcription	NH-A	brain
41	chr12:82864800-82869600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:82865200-82867000	Weak transcription	Left Ventricle	heart
43	chr12:82865400-82866800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:82865600-82867200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:82866000-82866800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:82866000-82866800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:82866200-82867200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:82866400-82867000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
49	chr12:82866600-82867000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:82866600-82867000	ZNF genes & repeats	Brain Anterior Caudate	brain

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