Variant report

Variant	rs10485696
Chromosome Location	chr20:41422460-41422461
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs114094	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs11697780	0.86[MEX][hapmap]
rs11699751	0.80[CHD][hapmap];0.91[MEX][hapmap]
rs17749217	0.92[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap]
rs17749365	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17749630	0.84[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs17811425	0.89[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.82[ASN][1000 genomes]
rs1885834	0.92[JPT][hapmap]
rs1973949	1.00[ASW][hapmap];0.85[CEU][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes]
rs208230	0.83[CHD][hapmap]
rs208250	0.85[JPT][hapmap]
rs208254	0.82[CEU][hapmap];0.92[JPT][hapmap]
rs57394208	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73098060	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73098063	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73098065	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73098070	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73099955	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73099959	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73099962	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs980929	0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][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	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10485696	SPINT4	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41417000-41424200	Weak transcription	Pancreas	Pancrea
2	chr20:41420000-41437600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr20:41421200-41427600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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