Variant report

Variant	rs12712692
Chromosome Location	chr2:40580065-40580066
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10165271	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10168748	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10178405	0.81[CHB][hapmap]
rs10192546	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10490051	0.81[CHB][hapmap]
rs11124739	0.84[ASN][1000 genomes]
rs11690171	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468092	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12987979	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12988856	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12989200	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12989852	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12995004	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12996962	0.81[CHB][hapmap]
rs13014950	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13022231	0.81[CHB][hapmap]
rs13031441	0.82[JPT][hapmap]
rs13032770	0.81[CHB][hapmap]
rs13405065	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1477004	0.81[CHB][hapmap]
rs1558654	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1558655	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2373857	0.85[CHB][hapmap]
rs4446101	0.85[CHB][hapmap]
rs4645043	0.81[CHB][hapmap]
rs4952409	0.85[CHB][hapmap]
rs6544323	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6544324	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544325	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6544326	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6544329	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6544330	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs6709574	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6738580	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6738673	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967351	0.85[CHB][hapmap]
rs981739	0.81[CHB][hapmap]
rs990270	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1010508	chr2:40526981-40590777	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv535655	chr2:40526981-40590777	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv873914	chr2:40573350-40586022	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40552800-40590600	Weak transcription	Fetal Kidney	kidney
2	chr2:40571600-40582600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:40574600-40586000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:40574600-40590600	Weak transcription	Aorta	Aorta
5	chr2:40576800-40587600	Weak transcription	NH-A	brain
6	chr2:40578200-40581200	Enhancers	HSMM	muscle
7	chr2:40578400-40580600	Enhancers	NHDF-Ad	bronchial
8	chr2:40578400-40581000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:40578400-40582000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:40578400-40583400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:40578600-40580600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:40578600-40580600	Enhancers	Osteobl	bone
13	chr2:40578600-40583000	Enhancers	Fetal Heart	heart
14	chr2:40578800-40580600	Enhancers	HMEC	breast
15	chr2:40578800-40580600	Enhancers	HSMMtube	muscle
16	chr2:40578800-40581000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:40578800-40581200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:40578800-40581600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr2:40579000-40580400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:40579200-40580200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:40579200-40580200	Enhancers	NHLF	lung
22	chr2:40579400-40580400	Enhancers	HUVEC	blood vessel
23	chr2:40579400-40582400	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:40579600-40586800	Enhancers	Colon Smooth Muscle	Colon
25	chr2:40579800-40580200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:40579800-40580200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:40579800-40580200	Enhancers	Right Ventricle	heart
28	chr2:40579800-40580200	Flanking Active TSS	Hela-S3	cervix
29	chr2:40579800-40581000	Enhancers	Right Atrium	heart
30	chr2:40579800-40581200	Enhancers	Adipose Nuclei	Adipose
31	chr2:40579800-40581800	Enhancers	Fetal Stomach	stomach
32	chr2:40579800-40582000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:40580000-40580200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr2:40580000-40580200	Enhancers	Psoas Muscle	Psoas
35	chr2:40580000-40580400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:40580000-40581200	Enhancers	Left Ventricle	heart
37	chr2:40580000-40581600	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links