Variant report

Variant	rs57560057
Chromosome Location	chr12:45657440-45657441
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	chr12:45608273..45611402-chr12:45650771..45657484,8	MCF-7	breast:
2	chr12:45655142..45658052-chr12:45658399..45661222,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134297	Chromatin interaction
ENSG00000177119	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10459293	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10459294	0.91[ASN][1000 genomes]
rs10459295	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10492284	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10748412	0.89[EUR][1000 genomes]
rs10785556	0.82[ASN][1000 genomes]
rs10880758	0.80[ASN][1000 genomes]
rs10880765	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10880766	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10880768	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11182898	0.80[ASN][1000 genomes]
rs11182899	0.82[ASN][1000 genomes]
rs11182903	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11182904	0.82[ASN][1000 genomes]
rs11182912	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11182916	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11182917	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11182919	0.87[ASN][1000 genomes]
rs11182921	0.89[ASN][1000 genomes]
rs11182923	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11182927	0.89[ASN][1000 genomes]
rs11182931	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11182935	0.90[ASN][1000 genomes]
rs11182940	0.89[ASN][1000 genomes]
rs11182941	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11182942	0.88[ASN][1000 genomes]
rs11182943	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11182947	0.92[ASN][1000 genomes]
rs11182953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182954	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182957	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11182961	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11182965	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11182966	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11182969	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11182970	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11182973	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11182974	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11182981	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11561532	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11610233	0.82[ASN][1000 genomes]
rs11611509	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11612203	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11612233	0.89[ASN][1000 genomes]
rs11614082	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11614089	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11615850	0.89[ASN][1000 genomes]
rs12226944	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12227678	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12228399	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12228733	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12299174	0.82[ASN][1000 genomes]
rs12320437	0.89[ASN][1000 genomes]
rs12322087	0.82[ASN][1000 genomes]
rs12814332	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12815115	0.88[ASN][1000 genomes]
rs12815334	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815577	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12815723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818421	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822746	0.89[ASN][1000 genomes]
rs12828052	0.86[ASN][1000 genomes]
rs17095551	0.89[ASN][1000 genomes]
rs17095557	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2408185	0.89[ASN][1000 genomes]
rs34024171	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34759896	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35032811	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35054776	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35400022	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35588430	0.82[ASN][1000 genomes]
rs3759077	0.89[ASN][1000 genomes]
rs3759081	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3759082	0.89[ASN][1000 genomes]
rs3782131	0.89[ASN][1000 genomes]
rs4768085	0.89[EUR][1000 genomes]
rs57797434	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61923810	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61923825	0.89[ASN][1000 genomes]
rs61923830	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7304481	0.89[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	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45636200-45662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:45651200-45662000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:45651400-45662000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:45651400-45662400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:45651400-45675600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:45651600-45662000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:45651600-45662400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:45651600-45667000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:45651600-45667400	Weak transcription	Brain Substantia Nigra	brain
10	chr12:45651600-45674000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:45653800-45662000	Weak transcription	Esophagus	oesophagus
12	chr12:45654200-45657800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:45654200-45662000	Weak transcription	Right Ventricle	heart
14	chr12:45654200-45662000	Weak transcription	Spleen	Spleen
15	chr12:45654200-45662400	Weak transcription	Gastric	stomach
16	chr12:45654200-45666800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:45654400-45661800	Weak transcription	A549	lung
18	chr12:45654400-45662000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:45654400-45662000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:45654400-45662000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:45654400-45662000	Weak transcription	Osteobl	bone
22	chr12:45654400-45662400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:45654400-45662400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:45654400-45662400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:45654400-45662400	Weak transcription	Fetal Stomach	stomach
26	chr12:45654400-45662400	Weak transcription	HSMM	muscle
27	chr12:45654400-45662400	Weak transcription	NH-A	brain
28	chr12:45654400-45662400	Weak transcription	NHLF	lung
29	chr12:45654400-45662600	Weak transcription	Stomach Mucosa	stomach
30	chr12:45654400-45666600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:45654400-45667600	Weak transcription	Primary T cells from cord blood	blood
32	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:45654600-45660800	Weak transcription	NHEK	skin
34	chr12:45654800-45661200	Weak transcription	HMEC	breast
35	chr12:45654800-45662000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:45655000-45659400	Weak transcription	Pancreas	Pancrea
37	chr12:45655000-45660400	Weak transcription	HUVEC	blood vessel
38	chr12:45655000-45662000	Weak transcription	Lung	lung
39	chr12:45655600-45660400	Weak transcription	Fetal Lung	lung
40	chr12:45655600-45661000	Weak transcription	Hela-S3	cervix
41	chr12:45655800-45657600	Weak transcription	HepG2	liver
42	chr12:45655800-45661800	Weak transcription	Adipose Nuclei	Adipose
43	chr12:45656000-45662000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:45656400-45659800	Enhancers	Fetal Intestine Large	intestine
45	chr12:45656600-45657600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:45656600-45657600	Enhancers	Aorta	Aorta
47	chr12:45656600-45657600	Enhancers	Left Ventricle	heart
48	chr12:45656600-45658200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:45656600-45658400	Enhancers	Fetal Intestine Small	intestine
50	chr12:45656600-45659200	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links