Variant report

Variant	rs17122689
Chromosome Location	chr12:60002284-60002285
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	chr12:59989176..59992374-chr12:59998507..60002701,5	MCF-7	breast:
2	chr12:59998248..60000809-chr12:60000863..60003196,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118596	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12824130	0.82[CEU][hapmap]
rs1497473	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122680	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122682	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122685	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122687	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17122718	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122739	1.00[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]
rs17122757	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122764	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17122766	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122781	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122783	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122785	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122790	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]
rs17122791	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122795	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122807	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs17122818	0.81[ASN][1000 genomes]
rs17122823	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122827	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122830	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122837	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122838	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122843	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122846	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122849	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17122850	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2706317	0.82[CEU][hapmap]
rs2706321	0.82[CEU][hapmap]
rs2711669	1.00[CEU][hapmap]
rs972132	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982321	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1038100	chr12:59983391-60018745	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr12:59991000-60005000	Weak transcription	Lung	lung
2	chr12:59991200-60004600	Weak transcription	Ovary	ovary
3	chr12:59991400-60004600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:59991400-60004600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:59991400-60004600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:59991400-60005000	Weak transcription	Pancreas	Pancrea
7	chr12:59991400-60009400	Weak transcription	Gastric	stomach
8	chr12:59991600-60003600	Weak transcription	Fetal Thymus	thymus
9	chr12:59991600-60004400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:59991600-60004600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:59991600-60004600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:59991600-60004600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:59991600-60004800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:59991600-60005000	Weak transcription	Thymus	Thymus
15	chr12:59991600-60009400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:59991800-60004800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:59992000-60004400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:59992000-60004600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:59992200-60004600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:59992400-60004600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:59992600-60013400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:59993800-60003200	Weak transcription	Right Ventricle	heart
23	chr12:59993800-60004600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:59993800-60004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:59994000-60005000	Weak transcription	NHLF	lung
26	chr12:59994200-60004800	Weak transcription	Fetal Heart	heart
27	chr12:59994400-60004800	Weak transcription	Adipose Nuclei	Adipose
28	chr12:59994600-60004600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:59994800-60004400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:59994800-60004400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr12:59994800-60005600	Weak transcription	Aorta	Aorta
32	chr12:59995600-60003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:59995800-60004400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:59997800-60004400	Weak transcription	NHDF-Ad	bronchial
35	chr12:59999200-60004400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:59999200-60005000	Weak transcription	Left Ventricle	heart
37	chr12:59999400-60004600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:59999400-60005200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:59999600-60003400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:59999600-60004400	Weak transcription	Primary T cells from cord blood	blood
41	chr12:59999600-60004400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:59999800-60003600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:60000400-60004200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:60000600-60003000	Weak transcription	Primary B cells from cord blood	blood
45	chr12:60002000-60002400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:60002200-60005600	Weak transcription	Fetal Stomach	stomach
47	chr12:60002200-60006000	ZNF genes & repeats	Dnd41	blood

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