Variant report

Variant	rs541098
Chromosome Location	chr15:34358325-34358326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34354339..34357870-chr15:34358322..34362266,6	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10152308	0.84[CEU][hapmap]
rs10152504	0.84[CEU][hapmap]
rs11634415	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12437606	0.80[ASN][1000 genomes]
rs12443077	0.84[ASN][1000 genomes]
rs12903907	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs12917116	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1436922	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17817764	1.00[CEU][hapmap]
rs2279423	0.84[ASN][1000 genomes]
rs2632073	0.80[ASN][1000 genomes]
rs2632077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2632110	0.80[ASN][1000 genomes]
rs2705338	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs34474029	0.82[EUR][1000 genomes]
rs35804445	0.85[EUR][1000 genomes]
rs3764237	1.00[CEU][hapmap]
rs4779652	0.83[TSI][hapmap]
rs4779656	0.86[TSI][hapmap]
rs4780203	0.84[EUR][1000 genomes]
rs483279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs486230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs488762	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs489349	1.00[CHD][hapmap]
rs489945	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs499167	0.91[CEU][hapmap]
rs514472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs519152	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs519210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs520935	1.00[CHD][hapmap]
rs554303	0.91[CEU][hapmap]
rs579975	0.91[CEU][hapmap]
rs62014670	0.93[EUR][1000 genomes]
rs62014671	0.93[EUR][1000 genomes]
rs62014673	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62014674	0.84[EUR][1000 genomes]
rs639860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs640291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs646339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs647721	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs685516	1.00[CHD][hapmap]
rs71464844	0.93[EUR][1000 genomes]
rs7163545	1.00[CHD][hapmap]
rs7168640	0.91[EUR][1000 genomes]
rs7175823	0.80[TSI][hapmap]
rs7175933	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs8029344	0.91[CEU][hapmap]
rs8030094	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs8033335	0.84[CEU][hapmap]
rs8033781	0.95[EUR][1000 genomes]
rs8035849	0.91[CEU][hapmap]
rs8037065	0.84[CEU][hapmap]
rs8039219	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9672432	0.80[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
rs541098	CHRM5	cis	cerebellum	SCAN
rs541098	OTUD7A	cis	cerebellum	SCAN
rs541098	CHRM5	cis	parietal	SCAN
rs541098	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34354200-34372400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:34354200-34375600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:34354200-34376400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:34354400-34379600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:34355000-34369000	Weak transcription	Liver	Liver
6	chr15:34357000-34358800	Enhancers	HMEC	breast
7	chr15:34357200-34358800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:34357600-34358800	Enhancers	NHEK	skin
9	chr15:34357800-34359000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:34358000-34358600	Strong transcription	Aorta	Aorta
11	chr15:34358000-34358800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:34358000-34358800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links