Variant report

Variant	rs12064888
Chromosome Location	chr1:78805511-78805512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10873977	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162465	1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12063386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12073067	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12093121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1328439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap]
rs1333068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17388032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17388283	1.00[ASN][1000 genomes]
rs2050804	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050805	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104621	0.91[CEU][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap]
rs3845364	0.82[ASN][1000 genomes]
rs4650449	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57245756	0.82[ASN][1000 genomes]
rs59929409	0.82[ASN][1000 genomes]
rs60824360	0.82[ASN][1000 genomes]
rs6424765	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658252	0.82[ASN][1000 genomes]
rs6672484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6674539	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677734	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679941	0.82[ASN][1000 genomes]
rs6685021	0.82[ASN][1000 genomes]
rs7521129	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550428	0.82[ASN][1000 genomes]
rs7552859	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv2763565	chr1:78774623-78809058	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1011898	chr1:78774623-78815799	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv482697	chr1:78786028-78935333	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78804600-78805600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:78804600-78806400	Enhancers	HMEC	breast
3	chr1:78804600-78806800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:78804600-78807000	Enhancers	Hela-S3	cervix
5	chr1:78804600-78808400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:78804800-78806000	Enhancers	NH-A	brain
7	chr1:78804800-78806600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:78804800-78806800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:78804800-78806800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:78804800-78807000	Enhancers	HUVEC	blood vessel
11	chr1:78805000-78805600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:78805000-78805600	Enhancers	A549	lung
13	chr1:78805000-78805600	Flanking Active TSS	Osteobl	bone
14	chr1:78805000-78805800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:78805000-78806200	Enhancers	HSMMtube	muscle
16	chr1:78805000-78806400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:78805000-78806400	Enhancers	HSMM	muscle
18	chr1:78805000-78807000	Enhancers	NHEK	skin
19	chr1:78805000-78819800	Weak transcription	Pancreas	Pancrea
20	chr1:78805200-78805600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:78805200-78806000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:78805200-78806200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:78805400-78805600	Flanking Active TSS	NHDF-Ad	bronchial
24	chr1:78805400-78805600	Flanking Active TSS	NHLF	lung
25	chr1:78805400-78807600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links