Variant report

Variant	rs2954980
Chromosome Location	chr12:11859548-11859549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009951	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs1009953	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs1009954	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10743967	0.92[EUR][1000 genomes]
rs10845407	0.86[EUR][1000 genomes]
rs10845408	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11054421	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054424	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054425	0.93[JPT][hapmap]
rs11054429	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11054433	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11054439	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11615175	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs12228191	0.87[EUR][1000 genomes]
rs17818461	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs17818498	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17818624	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2051525	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2187641	0.85[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2187642	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2416882	0.88[EUR][1000 genomes]
rs2416883	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2724588	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2724616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2724618	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2724633	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2724645	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs2724648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2856321	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2856322	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2856324	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2856344	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs2860431	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2900208	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4763719	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4763720	0.87[EUR][1000 genomes]
rs4763721	0.87[EUR][1000 genomes]
rs7488701	0.87[EUR][1000 genomes]
rs762717	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs972798	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11827400-11879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:11838800-11872200	Weak transcription	Primary T cells from cord blood	blood
3	chr12:11841800-11860200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:11841800-11867400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:11844200-11864600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:11848000-11872200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:11848400-11861200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:11848800-11861400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:11848800-11879600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:11849400-11865000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:11851200-11861000	Weak transcription	Primary B cells from cord blood	blood
12	chr12:11853000-11872000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:11853200-11870400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:11854800-11860200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:11854800-11872600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:11855000-11859600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:11855000-11859600	Weak transcription	Esophagus	oesophagus
18	chr12:11855200-11859600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:11855200-11859600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:11855200-11860000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:11855200-11860200	Weak transcription	Gastric	stomach
22	chr12:11855200-11861200	Weak transcription	Dnd41	blood
23	chr12:11855200-11862600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:11855200-11864000	Weak transcription	Adipose Nuclei	Adipose
25	chr12:11855200-11871800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:11855400-11868200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:11856200-11860200	Weak transcription	Placenta	Placenta
28	chr12:11856800-11859800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:11857000-11861200	Enhancers	Small Intestine	intestine
30	chr12:11857000-11861600	Enhancers	Stomach Mucosa	stomach
31	chr12:11857000-11861800	Strong transcription	Primary hematopoietic stem cells	blood
32	chr12:11857000-11876800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:11857200-11860600	Strong transcription	GM12878-XiMat	blood
34	chr12:11857600-11864200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr12:11857800-11859600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:11857800-11860200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:11857800-11860400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:11857800-11860800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:11857800-11860800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:11857800-11860800	Enhancers	Brain Anterior Caudate	brain
41	chr12:11857800-11860800	Enhancers	NHEK	skin
42	chr12:11857800-11861000	Enhancers	HMEC	breast
43	chr12:11857800-11865200	Enhancers	Colon Smooth Muscle	Colon
44	chr12:11858000-11859800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr12:11858000-11859800	Enhancers	Stomach Smooth Muscle	stomach
46	chr12:11858000-11860000	Enhancers	Rectal Smooth Muscle	rectum
47	chr12:11858000-11860800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:11858000-11861400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:11858000-11861400	Enhancers	Brain Hippocampus Middle	brain
50	chr12:11858000-11861600	Enhancers	Fetal Stomach	stomach

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