Variant report

Variant	rs11630209
Chromosome Location	chr15:41893120-41893121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11630972	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11634582	0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11634804	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11636523	0.86[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs1197671	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs1197705	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs12906666	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12914573	0.86[EUR][1000 genomes]
rs12917387	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs17676332	1.00[JPT][hapmap]
rs17677098	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs17677757	0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs17678310	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs17733703	0.84[EUR][1000 genomes]
rs2178003	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2925339	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs34040639	1.00[JPT][hapmap]
rs34802546	0.85[EUR][1000 genomes]
rs35698486	0.85[EUR][1000 genomes]
rs56217428	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57359439	0.84[EUR][1000 genomes]
rs57408990	0.84[EUR][1000 genomes]
rs58644077	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59096593	0.84[EUR][1000 genomes]
rs60526934	0.84[EUR][1000 genomes]
rs62003871	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003872	0.83[EUR][1000 genomes]
rs62003874	0.83[EUR][1000 genomes]
rs62003878	0.88[EUR][1000 genomes]
rs66593163	0.88[EUR][1000 genomes]
rs7163603	0.83[EUR][1000 genomes]
rs7167078	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7183061	0.84[EUR][1000 genomes]
rs8042809	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs9646193	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11630209	NDUFAF1	cis	parietal	SCAN
rs11630209	MAPKBP1	cis	parietal	SCAN
rs11630209	RPAP1	cis	parietal	SCAN
rs11630209	SNAP23	cis	parietal	SCAN
rs11630209	SPTBN5	cis	Artery Tibial	GTEx
rs11630209	CAPN3	cis	parietal	SCAN
rs11630209	SPTBN5	cis	lung	GTEx
rs11630209	SPTBN5	cis	cerebellum	SCAN
rs11630209	MAPKBP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41881200-41895800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:41889600-41895000	Weak transcription	K562	blood
3	chr15:41891200-41896000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:41891400-41896000	Weak transcription	Ovary	ovary
5	chr15:41892600-41893200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:41892600-41893200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:41892600-41893200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr15:41892800-41893200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:41892800-41893400	Enhancers	Fetal Heart	heart
10	chr15:41893000-41893400	Enhancers	Fetal Kidney	kidney
11	chr15:41893000-41896000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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