Variant report

Variant	rs12127930
Chromosome Location	chr1:62740065-62740066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10889316	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207950	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs11207951	0.94[ASN][1000 genomes]
rs11207952	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11579934	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs11583803	0.94[ASN][1000 genomes]
rs11584786	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043263	0.83[EUR][1000 genomes]
rs12125010	0.81[ASN][1000 genomes]
rs12127630	0.85[CEU][hapmap]
rs1325738	0.90[CHB][hapmap]
rs1886830	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1925825	0.90[CHB][hapmap]
rs2666467	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2765254	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2765255	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2765260	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2765262	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4609464	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4915810	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6664843	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6680736	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6691591	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6695520	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:62734200-62750800	Weak transcription	Gastric	stomach
4	chr1:62735800-62740600	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr1:62736400-62740400	Enhancers	Fetal Thymus	thymus
6	chr1:62736400-62741000	Strong transcription	HepG2	liver
7	chr1:62737000-62740600	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr1:62737600-62740600	Strong transcription	Fetal Intestine Small	intestine
9	chr1:62737600-62741800	Strong transcription	Placenta	Placenta
10	chr1:62737800-62742600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:62737800-62744400	Weak transcription	Fetal Intestine Large	intestine
12	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
14	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:62738400-62740600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:62738800-62740600	Genic enhancers	Fetal Muscle Leg	muscle
17	chr1:62739000-62740400	Strong transcription	Pancreas	Pancrea
18	chr1:62739200-62740400	Strong transcription	Adipose Nuclei	Adipose
19	chr1:62739200-62740600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:62739400-62740200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:62739400-62740400	Strong transcription	Fetal Lung	lung
22	chr1:62739400-62740800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:62739400-62740800	Genic enhancers	Fetal Stomach	stomach
24	chr1:62739600-62744200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:62739800-62740200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:62740000-62740400	Strong transcription	Liver	Liver
27	chr1:62740000-62741200	Enhancers	Fetal Heart	heart

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