Variant report

Variant	rs263566
Chromosome Location	chr9:17082525-17082526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10810711	0.83[AFR][1000 genomes]
rs10810718	1.00[CEU][hapmap]
rs10810719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs10810724	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10962836	0.93[EUR][1000 genomes]
rs10962841	0.81[AFR][1000 genomes]
rs10962843	0.93[EUR][1000 genomes]
rs10962844	0.93[EUR][1000 genomes]
rs10962852	0.94[EUR][1000 genomes]
rs10962855	0.99[EUR][1000 genomes]
rs10962860	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10962873	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10962875	0.91[EUR][1000 genomes]
rs1617507	0.80[AFR][1000 genomes]
rs1725365	0.82[AFR][1000 genomes]
rs1948107	0.83[AFR][1000 genomes]
rs1948108	0.82[AFR][1000 genomes]
rs2246	0.83[AFR][1000 genomes]
rs2450534	0.82[AFR][1000 genomes]
rs2462942	0.81[AFR][1000 genomes]
rs2481546	0.80[AFR][1000 genomes]
rs2481552	0.82[AFR][1000 genomes]
rs2492870	0.81[AFR][1000 genomes]
rs2632540	0.92[EUR][1000 genomes]
rs263562	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs263565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263618	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs263619	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs263620	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2774632	0.81[AFR][1000 genomes]
rs2815194	0.83[AFR][1000 genomes]
rs366216	0.83[YRI][hapmap]
rs368289	0.82[AFR][1000 genomes]
rs369822	0.82[AFR][1000 genomes]
rs375152	0.82[AFR][1000 genomes]
rs378128	0.82[AFR][1000 genomes]
rs378407	0.82[AFR][1000 genomes]
rs380977	0.82[AFR][1000 genomes]
rs381883	0.84[ASN][1000 genomes]
rs383580	0.82[AFR][1000 genomes]
rs386620	0.82[AFR][1000 genomes]
rs387903	0.83[AFR][1000 genomes]
rs388786	0.82[AFR][1000 genomes]
rs389432	0.81[AFR][1000 genomes]
rs389733	0.82[AFR][1000 genomes]
rs390114	0.82[AFR][1000 genomes]
rs390228	0.82[AFR][1000 genomes]
rs391156	0.82[AFR][1000 genomes]
rs398715	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs399430	0.83[AFR][1000 genomes]
rs400582	0.83[AFR][1000 genomes]
rs400972	0.83[AFR][1000 genomes]
rs404912	0.82[AFR][1000 genomes]
rs405039	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs411013	0.80[AFR][1000 genomes]
rs412190	0.80[AFR][1000 genomes]
rs420115	0.82[AFR][1000 genomes]
rs423395	0.83[AFR][1000 genomes]
rs425003	0.82[AFR][1000 genomes]
rs426761	0.83[AFR][1000 genomes]
rs427659	0.84[ASN][1000 genomes]
rs428654	0.83[AFR][1000 genomes]
rs430616	0.82[AFR][1000 genomes]
rs431059	0.82[AFR][1000 genomes]
rs431342	0.82[AFR][1000 genomes]
rs436873	0.82[AFR][1000 genomes]
rs441761	0.82[AFR][1000 genomes]
rs442431	0.83[AFR][1000 genomes]
rs447681	0.82[AFR][1000 genomes]
rs448576	0.83[AFR][1000 genomes]
rs450371	0.82[AFR][1000 genomes]
rs452396	0.80[AFR][1000 genomes]
rs453801	0.83[AFR][1000 genomes]
rs454019	0.82[AFR][1000 genomes]
rs503467	0.83[AFR][1000 genomes]
rs914049	0.83[AFR][1000 genomes]
rs914050	0.83[AFR][1000 genomes]
rs914051	0.83[AFR][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	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	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs263566	SLC24A2	cis	parietal	SCAN
rs263566	HAUS6	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17081200-17082800	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr9:17081400-17082800	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr9:17081400-17083000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr9:17081600-17082600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:17081600-17083000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr9:17081600-17083000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:17081600-17083000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:17081600-17083400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:17081600-17083400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:17081600-17083400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr9:17081800-17082800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr9:17081800-17083000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:17081800-17083000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr9:17081800-17083000	Enhancers	Fetal Kidney	kidney
15	chr9:17082200-17082800	Enhancers	Fetal Lung	lung
16	chr9:17082200-17083000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:17082400-17082800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:17082400-17082800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:17082400-17082800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:17082400-17082800	Enhancers	Colon Smooth Muscle	Colon
21	chr9:17082400-17082800	Enhancers	HSMM	muscle
22	chr9:17082400-17083400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:17082400-17083600	Enhancers	Osteobl	bone
24	chr9:17082400-17083800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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