Variant report

Variant	rs579975
Chromosome Location	chr15:34349224-34349225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10152308	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs10152504	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs12441615	0.84[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1436922	0.91[CEU][hapmap]
rs1529951	0.96[ASN][1000 genomes]
rs16958595	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs16958780	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs17817764	0.91[CEU][hapmap]
rs1968497	0.96[ASN][1000 genomes]
rs2705338	0.91[CEU][hapmap]
rs3764237	0.95[CEU][hapmap]
rs3764238	0.84[CHB][hapmap];0.90[CHD][hapmap]
rs499167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534155	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539584	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs554303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562486	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564262	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587714	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59502570	0.80[ASN][1000 genomes]
rs668922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175933	0.91[CEU][hapmap]
rs8029344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033335	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs8035849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037065	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs9707955	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs579975	CHRM5	cis	parietal	SCAN
rs579975	CHRM5	cis	cerebellum	SCAN
rs579975	AVEN	cis	lymphoblastoid	seeQTL
rs579975	CHRM5	cis	brain	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34348000-34349400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr15:34348000-34349600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:34348000-34350000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:34348000-34350000	Enhancers	Osteobl	bone
5	chr15:34348200-34349400	Enhancers	HMEC	breast
6	chr15:34348400-34349400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:34348400-34349400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:34348600-34349800	Enhancers	NH-A	brain
9	chr15:34348600-34350400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:34348800-34350400	Enhancers	Placenta	Placenta
11	chr15:34349000-34350000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:34349000-34353800	Weak transcription	HSMM	muscle
13	chr15:34349000-34358000	Weak transcription	Aorta	Aorta
14	chr15:34349200-34354000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:34349200-34357000	Weak transcription	NHEK	skin

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