Variant report

Variant	rs2642019
Chromosome Location	chr12:82841765-82841766
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	chr12:82819815..82822098-chr12:82840091..82842622,2	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10219540	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs10431469	0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs10732677	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10735451	0.84[EUR][1000 genomes]
rs10735454	1.00[CEU][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10735455	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10746241	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs10746242	0.82[YRI][hapmap]
rs10746243	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs10746245	0.83[YRI][hapmap]
rs10746247	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10746248	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10746250	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10746251	0.91[EUR][1000 genomes]
rs10778891	0.84[EUR][1000 genomes]
rs10778894	0.94[EUR][1000 genomes]
rs10778897	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs10778903	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs10778904	0.94[EUR][1000 genomes]
rs10778905	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs10778906	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[EUR][1000 genomes]
rs10778908	1.00[CEU][hapmap];0.94[YRI][hapmap];0.97[EUR][1000 genomes]
rs10862481	0.94[EUR][1000 genomes]
rs10862482	0.83[YRI][hapmap]
rs10862484	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10862485	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10862486	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11837949	0.83[EUR][1000 genomes]
rs1494023	0.80[YRI][hapmap]
rs1494024	0.83[YRI][hapmap]
rs17009470	0.94[EUR][1000 genomes]
rs17009622	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17009629	0.83[EUR][1000 genomes]
rs17719033	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17775000	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17775447	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17775501	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17776114	0.83[EUR][1000 genomes]
rs1874058	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2068633	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs2254688	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2401026	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2401027	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs2401032	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs2401034	0.80[YRI][hapmap]
rs2401039	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642010	0.80[YRI][hapmap]
rs2642015	1.00[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642018	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642021	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642023	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2717446	0.80[YRI][hapmap]
rs2717449	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2717459	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731286	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2731288	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731289	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731290	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731291	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731292	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731294	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731295	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731297	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28626834	0.94[EUR][1000 genomes]
rs2895910	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2895911	0.94[EUR][1000 genomes]
rs2895912	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs2895915	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs4143187	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4143190	0.84[EUR][1000 genomes]
rs41535250	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4242864	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4242870	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs4257045	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4284465	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4296098	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4334093	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4343090	1.00[CEU][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4356298	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4370996	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes]
rs4387422	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4399377	1.00[CEU][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4411333	0.85[YRI][hapmap]
rs4417379	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs4460874	0.94[EUR][1000 genomes]
rs4471506	0.84[EUR][1000 genomes]
rs4483662	0.84[EUR][1000 genomes]
rs4505128	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4516038	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4517594	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4540892	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs4553425	1.00[CEU][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4587790	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4628747	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4882379	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4882386	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4882389	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4882390	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4882435	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs4882438	0.94[EUR][1000 genomes]
rs4882541	0.94[EUR][1000 genomes]
rs4882542	0.88[EUR][1000 genomes]
rs55806388	0.94[EUR][1000 genomes]
rs55887136	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56337649	1.00[EUR][1000 genomes]
rs6539669	0.94[EUR][1000 genomes]
rs7133956	0.83[EUR][1000 genomes]
rs7294771	0.94[EUR][1000 genomes]
rs7294903	0.94[EUR][1000 genomes]
rs7297164	1.00[CEU][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7299307	0.88[EUR][1000 genomes]
rs7299616	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7304084	0.83[YRI][hapmap]
rs7309442	0.94[EUR][1000 genomes]
rs7311246	0.80[YRI][hapmap]
rs7313975	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315834	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs7316500	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs7488252	0.81[YRI][hapmap]
rs7953161	0.83[EUR][1000 genomes]
rs7953234	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7954119	0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7954460	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7969953	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7977443	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8181688	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[EUR][1000 genomes]
rs8181705	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82791200-82852000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:82803600-82852000	Weak transcription	Left Ventricle	heart
3	chr12:82804600-82869400	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:82822400-82862000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:82823000-82852400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:82823000-82862200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:82823200-82868000	Weak transcription	Brain Angular Gyrus	brain
8	chr12:82824200-82850000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:82824200-82868200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:82825200-82851400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:82826400-82843000	Weak transcription	Brain Substantia Nigra	brain
12	chr12:82826400-82844400	Weak transcription	Fetal Kidney	kidney
13	chr12:82827200-82862200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:82828600-82852200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:82831400-82862200	Weak transcription	Pancreas	Pancrea
16	chr12:82832000-82862400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:82832200-82855600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:82832200-82869600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:82832400-82873400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:82832600-82869800	Weak transcription	Gastric	stomach
21	chr12:82833000-82866800	Weak transcription	Lung	lung
22	chr12:82833200-82842800	Weak transcription	HUVEC	blood vessel
23	chr12:82833200-82866600	Weak transcription	Right Ventricle	heart
24	chr12:82833400-82862200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:82833400-82866800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:82834000-82874400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:82834200-82865000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:82834200-82866800	Weak transcription	Esophagus	oesophagus
29	chr12:82834200-82866800	Weak transcription	Spleen	Spleen
30	chr12:82834600-82853000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:82834600-82868200	Weak transcription	Colonic Mucosa	Colon
32	chr12:82836000-82851200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:82836200-82852000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:82836200-82852000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:82836200-82852200	Weak transcription	Fetal Intestine Large	intestine
36	chr12:82836400-82850200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:82836400-82851600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:82836400-82852000	Weak transcription	Primary T cells from cord blood	blood
39	chr12:82836400-82852200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr12:82836400-82853200	Weak transcription	Aorta	Aorta
41	chr12:82836400-82853600	Weak transcription	Brain Anterior Caudate	brain
42	chr12:82836400-82865000	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:82836400-82868400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:82836400-82870000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:82836600-82852600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr12:82837000-82868000	Weak transcription	Fetal Heart	heart
47	chr12:82837200-82842800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:82837600-82862200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:82837600-82865800	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:82837800-82876400	Weak transcription	Psoas Muscle	Psoas

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