Variant report

Variant	rs4912461
Chromosome Location	chr1:86547798-86547799
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11583563	0.90[CEU][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11588997	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11801529	0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap]
rs11802445	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564004	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12743345	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12744220	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744313	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12752769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12753548	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12754154	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1408666	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1698735	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs17406471	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17415366	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2221588	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2390052	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4522024	0.90[CHB][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.83[YRI][hapmap]
rs473232	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs474106	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs477862	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs485816	0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs4912462	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs494796	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs514185	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs541936	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs569541	0.83[EUR][1000 genomes]
rs582622	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs589343	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs633604	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs641712	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs645271	0.81[EUR][1000 genomes]
rs658313	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6665582	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs679734	0.81[CHB][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.83[YRI][hapmap]
rs695051	0.90[CHB][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap]
rs72716135	0.95[ASN][1000 genomes]
rs7514100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524738	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7545716	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7548696	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7552025	0.90[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525678	chr1:86487914-86549498	Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1797916	chr1:86529538-86556298	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1008311	chr1:86547606-86548372	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4912461	COL24A1	cis	Artery Tibial	GTEx
rs4912461	LOC339524	cis	cerebellum	SCAN
rs4912461	COL24A1	cis	lymphoblastoid	seeQTL
rs4912461	LOC339524	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86547000-86556800	Weak transcription	Pancreas	Pancrea
2	chr1:86547400-86553600	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links