Variant report

Variant	rs2254688
Chromosome Location	chr12:82834144-82834145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10219540	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs10431469	0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs10732677	1.00[EUR][1000 genomes]
rs10735451	0.84[EUR][1000 genomes]
rs10735453	0.80[YRI][hapmap]
rs10735454	1.00[CEU][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs10735455	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs10746241	0.94[YRI][hapmap];0.84[EUR][1000 genomes]
rs10746242	0.86[YRI][hapmap]
rs10746243	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs10746244	0.83[YRI][hapmap]
rs10746245	0.86[YRI][hapmap]
rs10746247	1.00[EUR][1000 genomes]
rs10746248	1.00[EUR][1000 genomes]
rs10746250	1.00[EUR][1000 genomes]
rs10746251	0.91[EUR][1000 genomes]
rs10778889	0.80[YRI][hapmap]
rs10778891	0.84[EUR][1000 genomes]
rs10778894	0.94[EUR][1000 genomes]
rs10778897	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs10778903	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs10778904	0.94[EUR][1000 genomes]
rs10778905	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs10778906	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs10778908	1.00[CEU][hapmap];0.88[YRI][hapmap];0.97[EUR][1000 genomes]
rs10862481	0.94[EUR][1000 genomes]
rs10862482	0.86[YRI][hapmap]
rs10862484	1.00[EUR][1000 genomes]
rs10862485	1.00[EUR][1000 genomes]
rs10862486	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs11837949	0.83[EUR][1000 genomes]
rs1494023	0.84[YRI][hapmap]
rs1494024	0.86[YRI][hapmap]
rs17009470	0.94[EUR][1000 genomes]
rs17009622	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17009629	0.83[EUR][1000 genomes]
rs17719033	1.00[CEU][hapmap];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];1.00[EUR][1000 genomes]
rs17776114	0.83[EUR][1000 genomes]
rs1874058	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2068633	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs2401026	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2401027	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs2401032	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs2401034	0.84[YRI][hapmap]
rs2401035	0.80[YRI][hapmap]
rs2401039	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs2642010	0.84[YRI][hapmap]
rs2642015	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2642017	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642018	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642019	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2642021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2642023	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2717446	0.84[YRI][hapmap];0.88[AFR][1000 genomes]
rs2717449	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs2717459	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs2731286	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2731288	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731289	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731290	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731291	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731292	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731294	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731295	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2731297	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28626834	0.94[EUR][1000 genomes]
rs2895910	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs2895911	0.94[EUR][1000 genomes]
rs2895912	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes]
rs2895915	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs4143187	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs4143190	0.84[EUR][1000 genomes]
rs41535250	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4242864	1.00[CEU][hapmap];0.81[YRI][hapmap];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	1.00[EUR][1000 genomes]
rs4296098	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs4334093	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4343090	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs4356298	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs4370996	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes]
rs4387422	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs4399377	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs4411333	0.90[YRI][hapmap]
rs4417379	1.00[CEU][hapmap];0.90[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];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs4516038	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4517594	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs4540892	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs4553425	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs4587790	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs4628747	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs4882379	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs4882386	1.00[EUR][1000 genomes]
rs4882389	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs4882390	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs4882435	1.00[CEU][hapmap];0.89[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	1.00[EUR][1000 genomes]
rs56337649	1.00[EUR][1000 genomes]
rs6539662	0.82[YRI][hapmap]
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];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs7299307	0.88[EUR][1000 genomes]
rs7299616	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs7304084	0.86[YRI][hapmap]
rs7309442	0.94[EUR][1000 genomes]
rs7311246	0.84[YRI][hapmap]
rs7313975	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs7315834	0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs7316500	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs7488252	0.85[YRI][hapmap]
rs7953161	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7953234	0.94[EUR][1000 genomes]
rs7954119	0.85[YRI][hapmap];0.94[EUR][1000 genomes]
rs7954460	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs7969953	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7977443	1.00[EUR][1000 genomes]
rs8181688	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs8181705	1.00[CEU][hapmap];0.90[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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82758400-82835600	Weak transcription	Psoas Muscle	Psoas
2	chr12:82783000-82838000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:82791200-82852000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:82793400-82834400	Weak transcription	Liver	Liver
5	chr12:82802200-82834400	Weak transcription	Aorta	Aorta
6	chr12:82802200-82834400	Weak transcription	Ovary	ovary
7	chr12:82803600-82852000	Weak transcription	Left Ventricle	heart
8	chr12:82804600-82869400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:82809600-82834400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:82819600-82835600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:82821000-82836200	Weak transcription	Fetal Heart	heart
12	chr12:82821200-82836800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:82822400-82862000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:82822800-82835600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:82823000-82852400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:82823000-82862200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:82823200-82834400	Weak transcription	Fetal Intestine Large	intestine
18	chr12:82823200-82868000	Weak transcription	Brain Angular Gyrus	brain
19	chr12:82824200-82850000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:82824200-82868200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:82825200-82851400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:82826000-82835600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:82826400-82843000	Weak transcription	Brain Substantia Nigra	brain
24	chr12:82826400-82844400	Weak transcription	Fetal Kidney	kidney
25	chr12:82827200-82862200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:82827400-82837600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:82828400-82835800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:82828600-82835800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:82828600-82852200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:82828800-82834400	Weak transcription	Brain Anterior Caudate	brain
31	chr12:82829000-82835600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:82829600-82836200	Weak transcription	HSMMtube	muscle
33	chr12:82830000-82836200	Weak transcription	Fetal Lung	lung
34	chr12:82830000-82836800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:82830200-82836800	Weak transcription	HSMM	muscle
36	chr12:82831400-82862200	Weak transcription	Pancreas	Pancrea
37	chr12:82831800-82841200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:82832000-82834400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:82832000-82837000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:82832000-82840000	Strong transcription	Adipose Nuclei	Adipose
41	chr12:82832000-82862400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:82832200-82834600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:82832200-82855600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:82832200-82869600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:82832400-82873400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:82832600-82834200	Weak transcription	Dnd41	blood
47	chr12:82832600-82837200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:82832600-82869800	Weak transcription	Gastric	stomach
49	chr12:82833000-82834600	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:82833000-82836200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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