Variant report

Variant	rs10962853
Chromosome Location	chr9:17076367-17076368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10810709	0.84[ASN][1000 genomes]
rs10810718	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs10810719	0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap]
rs10810724	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs10962836	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10962843	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10962844	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10962852	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10962855	0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10962860	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10962873	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs10962875	0.84[ASN][1000 genomes]
rs10962903	1.00[CHB][hapmap]
rs2632540	0.84[ASN][1000 genomes]
rs263562	0.81[EUR][1000 genomes]
rs263619	0.91[CEU][hapmap]
rs398715	1.00[EUR][1000 genomes]
rs405039	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892656	chr9:17008137-17076367	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv892657	chr9:17008137-17223492	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1033462	chr9:17046823-17081683	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1019424	chr9:17049320-17081683	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10962853	HAUS6	cis	parietal	SCAN
rs10962853	SLC24A2	cis	parietal	SCAN
rs10962853	PLIN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17065000-17078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:17075600-17076800	Enhancers	Fetal Kidney	kidney
3	chr9:17076000-17076600	Enhancers	Muscle Satellite Cultured Cells	--

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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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