Variant report

Variant	rs6791012
Chromosome Location	chr3:144492294-144492295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1512781	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16855936	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855937	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855941	0.97[ASN][1000 genomes]
rs16855943	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16855946	0.91[JPT][hapmap]
rs16855950	1.00[ASN][1000 genomes]
rs16855955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1916250	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1916251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2375565	1.00[CEU][hapmap]
rs56380437	1.00[ASN][1000 genomes]
rs56807652	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59664363	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60322313	0.91[ASN][1000 genomes]
rs60535604	0.98[ASN][1000 genomes]
rs60705164	0.91[ASN][1000 genomes]
rs61400914	0.91[ASN][1000 genomes]
rs61429069	0.91[ASN][1000 genomes]
rs61465948	0.91[ASN][1000 genomes]
rs6440267	0.91[ASN][1000 genomes]
rs6771295	0.91[ASN][1000 genomes]
rs6782105	0.91[ASN][1000 genomes]
rs6790055	1.00[ASN][1000 genomes]
rs6790749	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791002	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793649	0.91[ASN][1000 genomes]
rs6803084	1.00[ASN][1000 genomes]
rs6803703	1.00[CEU][hapmap]
rs73008056	0.91[ASN][1000 genomes]
rs7340591	0.91[ASN][1000 genomes]
rs73873579	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611272	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7615860	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630559	0.91[ASN][1000 genomes]
rs7635998	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636179	0.95[ASN][1000 genomes]
rs7636248	0.95[ASN][1000 genomes]
rs7639659	0.83[EUR][1000 genomes]
rs7641230	0.98[ASN][1000 genomes]
rs7641244	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641516	0.98[ASN][1000 genomes]
rs7644542	0.90[JPT][hapmap]
rs7646035	0.91[ASN][1000 genomes]
rs7651550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591928	chr3:144050897-144822081	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3357831	chr3:144433846-144790831	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3405013	chr3:144433866-144790801	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv829746	chr3:144451478-144618224	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv829747	chr3:144463330-144654092	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv999196	chr3:144487765-144529406	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv536755	chr3:144487765-144529406	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6791012	PCOLCE2	cis	cerebellum	SCAN
rs6791012	ZFYVE19	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:144489200-144492400	Enhancers	Brain Cingulate Gyrus	brain
2	chr3:144489800-144492400	Enhancers	HUVEC	blood vessel
3	chr3:144490600-144492600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:144491000-144496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:144491200-144493800	Weak transcription	Fetal Kidney	kidney
6	chr3:144491600-144493400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:144491600-144493600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:144491600-144493800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:144491600-144494000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:144492200-144493400	Weak transcription	NHDF-Ad	bronchial
11	chr3:144492200-144493800	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links