Variant report

Variant	rs17122790
Chromosome Location	chr12:60050575-60050576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1497473	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122680	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122682	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122685	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122687	0.85[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17122689	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122718	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122739	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122757	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122764	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17122766	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122781	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122783	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122785	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122791	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122795	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122807	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs17122818	0.81[ASN][1000 genomes]
rs17122823	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122827	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122830	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122837	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122838	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122843	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122846	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122849	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122850	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2711669	0.85[CEU][hapmap]
rs972132	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982321	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60013600-60055400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:60026600-60089200	Weak transcription	Gastric	stomach
3	chr12:60028200-60051400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:60029600-60063200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:60031800-60050600	Weak transcription	Spleen	Spleen
6	chr12:60034000-60061600	Weak transcription	Aorta	Aorta
7	chr12:60040600-60052400	Weak transcription	Lung	lung
8	chr12:60040600-60054000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:60040800-60054000	Weak transcription	Fetal Thymus	thymus
10	chr12:60041200-60051400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:60043400-60054000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:60044600-60054600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:60044800-60052000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:60044800-60055000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:60045000-60058400	Weak transcription	Left Ventricle	heart
16	chr12:60045600-60061600	Weak transcription	Pancreas	Pancrea
17	chr12:60045600-60071800	Weak transcription	Ovary	ovary
18	chr12:60045800-60051200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:60045800-60051200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:60045800-60051200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:60045800-60051400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:60045800-60054400	Weak transcription	Osteobl	bone
23	chr12:60045800-60085400	Weak transcription	NHDF-Ad	bronchial
24	chr12:60045800-60099800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:60046200-60051200	Weak transcription	Fetal Heart	heart
26	chr12:60046400-60051200	Weak transcription	HMEC	breast
27	chr12:60046400-60051400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:60046400-60054800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:60046600-60058000	Weak transcription	Adipose Nuclei	Adipose
30	chr12:60048400-60053600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:60048600-60050600	Strong transcription	Primary T cells from cord blood	blood
32	chr12:60048800-60050600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr12:60048800-60056200	Weak transcription	GM12878-XiMat	blood
34	chr12:60048800-60058400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:60049800-60051800	Strong transcription	Primary B cells from cord blood	blood
36	chr12:60050000-60050600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:60050000-60050800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:60050000-60050800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:60050000-60052200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:60050000-60068600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:60050200-60050600	Enhancers	NH-A	brain
42	chr12:60050200-60054000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:60050400-60050600	Enhancers	Right Ventricle	heart
44	chr12:60050400-60053400	Weak transcription	Dnd41	blood
45	chr12:60050400-60054000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:60050400-60060200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:60050400-60060400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links