Variant report

Variant	rs7961964
Chromosome Location	chr12:64330646-64330647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64329679..64331420-chr12:64342919..64345262,2	MCF-7	breast:
2	chr12:64238646..64240219-chr12:64329765..64332123,2	MCF-7	breast:
3	chr12:64323494..64326603-chr12:64329507..64332954,4	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12296441	1.00[EUR][1000 genomes]
rs12302441	1.00[EUR][1000 genomes]
rs12307017	1.00[EUR][1000 genomes]
rs12313251	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12315032	1.00[EUR][1000 genomes]
rs12316287	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12318085	1.00[EUR][1000 genomes]
rs12320688	1.00[EUR][1000 genomes]
rs17099997	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17100007	1.00[EUR][1000 genomes]
rs17100009	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17100013	1.00[EUR][1000 genomes]
rs55801058	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56236229	0.91[AFR][1000 genomes]
rs57074356	1.00[EUR][1000 genomes]
rs57138272	1.00[EUR][1000 genomes]
rs57140731	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57540857	1.00[EUR][1000 genomes]
rs57937852	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58129443	1.00[EUR][1000 genomes]
rs59161915	1.00[EUR][1000 genomes]
rs60392489	1.00[EUR][1000 genomes]
rs74097504	1.00[EUR][1000 genomes]
rs74097515	1.00[EUR][1000 genomes]
rs74097516	1.00[EUR][1000 genomes]
rs74097517	1.00[EUR][1000 genomes]
rs74097545	1.00[EUR][1000 genomes]
rs74097547	1.00[EUR][1000 genomes]
rs74099369	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099375	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099376	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099377	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099378	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099379	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099380	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099381	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099382	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099383	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099384	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099385	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099392	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099393	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099395	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099398	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74099400	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7961633	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7976142	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7976369	0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7977480	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7961964	AHSP	trans	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64298800-64334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:64312400-64331600	Weak transcription	Right Atrium	heart
3	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
4	chr12:64312800-64331200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:64312800-64331400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:64313000-64334400	Weak transcription	Psoas Muscle	Psoas
7	chr12:64313200-64331600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:64313200-64331600	Weak transcription	Left Ventricle	heart
9	chr12:64313200-64334400	Weak transcription	Pancreas	Pancrea
10	chr12:64314200-64331200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:64316600-64338400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:64319000-64331200	Weak transcription	Brain Anterior Caudate	brain
13	chr12:64319800-64331600	Weak transcription	Right Ventricle	heart
14	chr12:64323000-64331200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:64323000-64333800	Weak transcription	Ovary	ovary
16	chr12:64323400-64331600	Weak transcription	A549	lung
17	chr12:64324600-64333200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:64325400-64331400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:64325400-64334200	Weak transcription	Fetal Lung	lung
20	chr12:64325400-64334200	Weak transcription	NH-A	brain
21	chr12:64325400-64334400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:64325600-64331200	Weak transcription	Fetal Brain Female	brain
23	chr12:64325800-64330800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:64325800-64331600	Weak transcription	HSMMtube	muscle
25	chr12:64325800-64331600	Weak transcription	NHLF	lung
26	chr12:64325800-64331800	Weak transcription	HSMM	muscle
27	chr12:64326000-64331600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:64327600-64332600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:64328000-64339800	Enhancers	Fetal Brain Male	brain
30	chr12:64328200-64334400	Weak transcription	Lung	lung
31	chr12:64328400-64339600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:64328600-64331400	Enhancers	NHDF-Ad	bronchial
33	chr12:64328600-64334200	Weak transcription	Brain Germinal Matrix	brain
34	chr12:64328800-64331600	Weak transcription	NHEK	skin
35	chr12:64328800-64360800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:64329000-64331600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:64329000-64332200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:64329000-64336400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:64329000-64342200	Weak transcription	Hela-S3	cervix
40	chr12:64329400-64332200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:64329400-64339400	Weak transcription	HMEC	breast
42	chr12:64329600-64331600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:64329600-64333800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:64329800-64333200	Weak transcription	HUVEC	blood vessel
45	chr12:64329800-64343800	Weak transcription	Osteobl	bone
46	chr12:64330000-64331400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:64330000-64331600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:64330000-64342000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:64330000-64343800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:64330200-64338400	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links