Variant report

Variant	rs10889316
Chromosome Location	chr1:62746646-62746647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11207950	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11207951	0.87[ASN][1000 genomes]
rs11207952	0.83[ASN][1000 genomes]
rs11579934	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11583803	0.86[ASN][1000 genomes]
rs11584786	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12043263	0.88[EUR][1000 genomes]
rs12125010	0.87[ASN][1000 genomes]
rs12127630	0.85[CEU][hapmap]
rs12127930	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]
rs1325738	0.95[CHB][hapmap]
rs1886830	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1925825	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2666467	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2765254	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2765255	0.95[CHB][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2765260	0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2765262	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3850633	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3903928	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4609464	0.89[ASN][1000 genomes]
rs4915810	0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6664843	0.83[ASN][1000 genomes]
rs6680736	0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6691591	0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6695520	0.87[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	chr1:62734200-62750800	Weak transcription	Gastric	stomach
3	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:62743200-62746800	Weak transcription	HMEC	breast
6	chr1:62743200-62747800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:62744800-62747600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:62744800-62750800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:62745000-62747000	Strong transcription	HepG2	liver
10	chr1:62745600-62749200	Weak transcription	Fetal Thymus	thymus
11	chr1:62745800-62748600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:62746200-62747200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:62746400-62746800	Genic enhancers	Fetal Stomach	stomach
14	chr1:62746400-62747000	Strong transcription	Fetal Kidney	kidney
15	chr1:62746400-62747200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:62746400-62747200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:62746400-62747200	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr1:62746400-62747200	Strong transcription	Liver	Liver
19	chr1:62746400-62747400	ZNF genes & repeats	Fetal Muscle Leg	muscle
20	chr1:62746400-62747600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:62746400-62748000	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr1:62746400-62748800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:62746400-62749000	Weak transcription	Fetal Heart	heart
24	chr1:62746600-62746800	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr1:62746600-62747000	ZNF genes & repeats	Placenta	Placenta
26	chr1:62746600-62747400	ZNF genes & repeats	Fetal Lung	lung
27	chr1:62746600-62747400	Strong transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links