Variant report

Variant	rs2538966
Chromosome Location	chr7:147598261-147598262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10488348	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10952715	0.84[JPT][hapmap]
rs17234278	0.89[JPT][hapmap]
rs17236239	0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17236877	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17827310	0.86[ASN][1000 genomes]
rs2538967	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2538968	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2538970	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs2708267	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2710115	0.82[LWK][hapmap]
rs4397315	0.87[ASN][1000 genomes]
rs4431524	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4725752	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs56073287	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56265348	0.91[ASN][1000 genomes]
rs56335186	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57536589	0.87[ASN][1000 genomes]
rs62474777	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62481197	0.82[ASN][1000 genomes]
rs62481219	0.87[ASN][1000 genomes]
rs6972811	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs73166262	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7778252	0.96[CEU][hapmap]
rs851708	0.89[JPT][hapmap]
rs9655720	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2538966	ATG9B	cis	parietal	SCAN
rs2538966	OR6B1	cis	cerebellum	SCAN
rs2538966	PDGFRA	trans	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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