Variant report

Variant	rs9864105
Chromosome Location	chr3:54418601-54418602
allele	A/G
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]
rs11709302	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11711662	0.88[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs13082754	0.82[JPT][hapmap]
rs1375521	0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1375522	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1449330	0.88[GIH][hapmap];0.83[TSI][hapmap]
rs1449331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1473348	0.87[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2359785	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445653	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs6445655	0.85[JPT][hapmap]
rs6777368	0.81[AFR][1000 genomes]
rs6804196	0.82[ASW][hapmap];0.82[MEX][hapmap]
rs731508	0.83[ASW][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7372585	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7374435	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7426795	0.86[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7645545	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653648	0.88[CEU][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs9817603	0.94[ASW][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs9826277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843412	0.94[ASW][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9851130	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs9862712	0.88[GIH][hapmap];0.83[TSI][hapmap]
rs9862718	0.88[GIH][hapmap];0.83[TSI][hapmap]
rs9874831	0.83[AFR][1000 genomes];0.86[AMR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	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
rs9864105	TKT	cis	parietal	SCAN
rs9864105	SEMA3G	cis	parietal	SCAN
rs9864105	PCBP4	cis	parietal	SCAN
rs9864105	HESX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54411200-54423400	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links