Variant report

Variant	rs12313929
Chromosome Location	chr12:46875098-46875099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46764328..46767954-chr12:46874214..46878193,4	K562	blood:
2	chr12:46872950..46875847-chr12:46879914..46883290,3	K562	blood:
3	chr12:46867765..46869816-chr12:46873759..46876324,2	K562	blood:
4	chr12:46780258..46781885-chr12:46874855..46877387,2	MCF-7	breast:
5	chr12:46865908..46869326-chr12:46872874..46876694,4	MCF-7	breast:
6	chr12:46871245..46874397-chr12:46874774..46877643,3	MCF-7	breast:
7	chr12:46764655..46767393-chr12:46875079..46878516,5	K562	blood:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000257496	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10748448	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10748450	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10785628	0.85[AMR][1000 genomes]
rs10785629	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10880973	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10880974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183486	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs11183502	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183503	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11183504	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11837427	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12314541	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12321960	0.81[YRI][hapmap]
rs12824565	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12827740	0.83[AMR][1000 genomes]
rs2252238	0.95[CEU][hapmap]
rs3925101	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3935048	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4077707	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4077708	0.85[AMR][1000 genomes]
rs4768118	0.80[CHB][hapmap]
rs4768123	0.85[AMR][1000 genomes]
rs4768699	0.90[JPT][hapmap]
rs4768723	0.85[AMR][1000 genomes]
rs4768724	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768725	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768726	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4768727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768728	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768729	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768733	0.95[CEU][hapmap]
rs6582645	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6582657	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6582658	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6582659	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582660	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486915	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488577	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7953339	0.92[YRI][hapmap]
rs7954645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959731	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7960808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980455	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9669404	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9706162	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9706460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9706520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9971879	0.91[CHB][hapmap];0.95[JPT][hapmap]

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	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:46864200-46877400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:46864400-46877400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:46865400-46879200	Weak transcription	Right Ventricle	heart
5	chr12:46867800-46875800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:46868000-46876200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:46868000-46876200	Weak transcription	Primary B cells from cord blood	blood
8	chr12:46868000-46876400	Weak transcription	K562	blood
9	chr12:46868000-46881200	Weak transcription	GM12878-XiMat	blood
10	chr12:46868000-46883200	Weak transcription	Fetal Heart	heart
11	chr12:46868200-46877400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:46868200-46879200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:46868600-46877400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:46868600-46877400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr12:46868600-46877600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:46868600-46877600	Weak transcription	Ovary	ovary
17	chr12:46868600-46883000	Weak transcription	Left Ventricle	heart
18	chr12:46868600-46883400	Weak transcription	Psoas Muscle	Psoas
19	chr12:46868600-46889200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:46868800-46876600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:46868800-46883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:46868800-46886000	Weak transcription	HSMMtube	muscle
23	chr12:46869200-46876400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:46869200-46876800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:46870400-46880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:46871200-46887800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr12:46872000-46876400	Weak transcription	A549	lung
28	chr12:46872000-46876600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:46872000-46876800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:46872000-46877600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:46872000-46877600	Weak transcription	NHLF	lung
32	chr12:46872200-46875800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:46872800-46875600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:46873000-46877600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr12:46873000-46880400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:46873200-46876200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:46873200-46876600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:46873600-46875800	Weak transcription	HepG2	liver
39	chr12:46873600-46886000	Weak transcription	HSMM	muscle
40	chr12:46873800-46875600	Enhancers	Hela-S3	cervix
41	chr12:46874000-46875400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:46874000-46875400	Enhancers	HUVEC	blood vessel
43	chr12:46874000-46880400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:46874600-46877600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:46874800-46876400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:46874800-46876800	Weak transcription	Osteobl	bone
47	chr12:46874800-46877200	Weak transcription	NHDF-Ad	bronchial
48	chr12:46874800-46877400	Weak transcription	NHEK	skin
49	chr12:46874800-46883400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:46875000-46876200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links