Variant report

Variant	rs12075195
Chromosome Location	chr1:173065003-173065004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10798255	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12060864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118211	0.83[ASN][1000 genomes]
rs12142166	0.83[ASN][1000 genomes]
rs2223517	0.89[EUR][1000 genomes]
rs59105298	0.90[EUR][1000 genomes]
rs720455	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs975074	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs997331	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831904	chr1:172912110-173070429	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv533953	chr1:172939335-173133255	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12075195	PRDX6	cis	parietal	SCAN
rs12075195	TNFSF18	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173062400-173066600	Enhancers	NHDF-Ad	bronchial
2	chr1:173062600-173066400	Enhancers	HMEC	breast
3	chr1:173063000-173066400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:173063200-173066000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:173063400-173065200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:173063800-173066200	Enhancers	HSMM	muscle
7	chr1:173064000-173066400	Enhancers	Osteobl	bone
8	chr1:173064200-173065400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:173064200-173066400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:173064200-173066600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:173064400-173066200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:173064400-173066400	Enhancers	HSMMtube	muscle
13	chr1:173064400-173066600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:173064600-173065200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:173064600-173065400	Enhancers	NH-A	brain
16	chr1:173064600-173065400	Enhancers	NHEK	skin
17	chr1:173064600-173065400	Enhancers	NHLF	lung
18	chr1:173064600-173066400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:173064600-173066400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:173064600-173066400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:173064800-173065200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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