Variant report

Variant	rs10002500
Chromosome Location	chr4:47958679-47958680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10014206	0.86[EUR][1000 genomes]
rs10461076	0.81[ASN][1000 genomes]
rs10517200	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs10517204	0.93[ASW][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.86[YRI][hapmap]
rs10805163	0.93[ASW][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap]
rs11733288	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs12504018	0.90[YRI][hapmap]
rs12645164	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12645245	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs12645873	0.92[EUR][1000 genomes]
rs12651301	0.90[YRI][hapmap]
rs1371729	0.86[ASW][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs1371732	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1396051	0.93[ASW][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs1440228	0.91[YRI][hapmap]
rs1507913	0.83[AFR][1000 genomes]
rs1507914	0.83[AFR][1000 genomes]
rs17601719	0.92[EUR][1000 genomes]
rs17654502	0.92[EUR][1000 genomes]
rs17654526	0.91[EUR][1000 genomes]
rs1866688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1866689	0.86[ASW][hapmap];0.91[YRI][hapmap]
rs1899060	0.83[AFR][1000 genomes]
rs224800	0.83[AFR][1000 genomes]
rs2352470	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs2581493	0.81[AFR][1000 genomes]
rs2661513	1.00[YRI][hapmap]
rs28392911	0.92[EUR][1000 genomes]
rs28642966	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28699496	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28806296	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3113881	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs3113882	0.83[AFR][1000 genomes]
rs321623	0.92[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.91[YRI][hapmap]
rs321633	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap]
rs321644	0.81[AFR][1000 genomes]
rs321646	0.83[AFR][1000 genomes]
rs3950558	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs4694880	0.81[JPT][hapmap];0.86[YRI][hapmap]
rs55684720	0.92[EUR][1000 genomes]
rs6447603	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap]
rs6815011	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6823184	0.91[YRI][hapmap]
rs6823698	0.86[ASW][hapmap];0.91[YRI][hapmap]
rs6858440	0.86[ASW][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap]
rs73814824	0.86[EUR][1000 genomes]
rs978094	0.91[YRI][hapmap]
rs9994204	0.92[EUR][1000 genomes]
rs9995122	0.93[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv967291	chr4:47954000-47981934	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10002500	CNGA1	cis	Nerve Tibial	GTEx
rs10002500	CNGA1	cis	Muscle Skeletal	GTEx
rs10002500	CORIN	cis	Whole Blood	GTEx
rs10002500	NFXL1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47954600-47959200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links