Variant report

Variant	rs12090237
Chromosome Location	chr1:154389741-154389742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154389348..154391422-chr1:154394906..154397857,2	MCF-7	breast:
2	chr1:154376615..154383856-chr1:154388009..154396723,15	MCF-7	breast:
3	chr1:154376358..154381143-chr1:154387661..154394028,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction
ENSG00000228013	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11264221	1.00[MEX][hapmap]
rs1488085	1.00[CEU][hapmap]
rs16835877	1.00[CEU][hapmap]
rs34806329	1.00[EUR][1000 genomes]
rs55886061	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677920	1.00[MEX][hapmap]
rs6690277	1.00[MEX][hapmap]
rs72698116	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72698118	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72698123	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72698126	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72698128	1.00[EUR][1000 genomes]
rs7411976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154381000-154390800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:154381000-154390800	Weak transcription	NHLF	lung
3	chr1:154381200-154390800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:154381400-154390400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:154381400-154390600	Weak transcription	NHDF-Ad	bronchial
6	chr1:154381600-154390200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:154382000-154390800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:154382000-154390800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:154382400-154391600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:154382600-154390600	Weak transcription	Brain Angular Gyrus	brain
11	chr1:154383000-154390000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:154383400-154390800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:154383600-154391200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:154384200-154389800	Weak transcription	NHEK	skin
16	chr1:154384200-154390000	Weak transcription	HMEC	breast
17	chr1:154384200-154392000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:154384400-154390800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:154385800-154390600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:154386000-154391000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:154386200-154390600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:154386400-154390600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:154386400-154391200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:154386600-154390800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:154387000-154390000	Enhancers	Brain Anterior Caudate	brain
26	chr1:154387000-154390800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:154387000-154390800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:154387400-154390400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:154387400-154390800	Weak transcription	Primary T cells from cord blood	blood
30	chr1:154387400-154391000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:154387600-154390800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:154387600-154390800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:154387600-154390800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:154387600-154391000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:154387800-154389800	Enhancers	GM12878-XiMat	blood
36	chr1:154387800-154391200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:154388000-154390400	Enhancers	Liver	Liver
38	chr1:154388600-154389800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:154388600-154391000	Weak transcription	Fetal Intestine Small	intestine
40	chr1:154388600-154394200	Enhancers	Left Ventricle	heart
41	chr1:154388800-154391200	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:154388800-154391400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:154388800-154392200	Enhancers	Colon Smooth Muscle	Colon
44	chr1:154389000-154389800	Enhancers	Brain Substantia Nigra	brain
45	chr1:154389000-154390000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:154389000-154390000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:154389000-154390000	Enhancers	Gastric	stomach
48	chr1:154389000-154390200	Enhancers	Right Atrium	heart
49	chr1:154389000-154390800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:154389000-154390800	Enhancers	HepG2	liver

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