Variant report

Variant	rs2457637
Chromosome Location	chr9:15533394-15533395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10118359	0.80[EUR][1000 genomes]
rs10121591	0.81[EUR][1000 genomes]
rs10481557	0.81[CEU][hapmap]
rs10733295	0.93[CEU][hapmap];0.87[TSI][hapmap]
rs10738399	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10756671	0.81[CEU][hapmap]
rs10756673	0.83[EUR][1000 genomes]
rs10756674	0.81[CEU][hapmap]
rs10756677	0.81[CEU][hapmap]
rs10756687	0.81[CEU][hapmap]
rs10756688	0.81[CEU][hapmap]
rs10756689	0.81[CEU][hapmap]
rs10756690	0.81[CEU][hapmap]
rs10810397	0.93[CEU][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810399	0.81[CEU][hapmap]
rs10810401	0.81[CEU][hapmap]
rs10810408	0.81[CEU][hapmap]
rs10810416	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs10810419	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs10810422	0.82[EUR][1000 genomes]
rs10810424	0.80[EUR][1000 genomes]
rs10810426	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs10810427	0.93[CEU][hapmap]
rs10810428	0.81[CEU][hapmap]
rs10810429	0.93[CEU][hapmap]
rs10962066	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs10962070	0.81[CEU][hapmap]
rs10962098	0.81[CEU][hapmap]
rs10962099	0.81[CEU][hapmap]
rs10962106	0.81[EUR][1000 genomes]
rs10962126	0.93[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs11792937	0.84[EUR][1000 genomes]
rs13301516	0.84[EUR][1000 genomes]
rs1355171	0.93[CEU][hapmap];0.89[TSI][hapmap]
rs1396706	0.85[CEU][hapmap]
rs1533040	0.81[CEU][hapmap]
rs169342	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs1828383	0.81[AFR][1000 genomes]
rs183928	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1848582	0.83[EUR][1000 genomes]
rs192466	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2055772	0.81[CEU][hapmap]
rs2175080	0.89[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs2457265	0.81[EUR][1000 genomes]
rs2663300	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs276435	0.92[CEU][hapmap]
rs276436	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs276444	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs276447	0.83[AMR][1000 genomes]
rs276448	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs276449	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs276453	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs276454	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs276455	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2821545	0.84[ASW][hapmap];0.85[CEU][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs3119699	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs3122702	0.83[EUR][1000 genomes]
rs432452	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs433849	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs442549	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs451878	0.93[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4740614	0.89[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4740615	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs4740619	0.81[CEU][hapmap]
rs4741519	0.81[CEU][hapmap]
rs4741528	0.81[CEU][hapmap]
rs58607272	0.81[AFR][1000 genomes]
rs6474930	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6474931	0.80[CEU][hapmap]
rs6474944	0.81[CEU][hapmap]
rs6474945	0.81[CEU][hapmap]
rs6474946	0.80[EUR][1000 genomes]
rs6474951	0.89[CEU][hapmap]
rs6474952	0.89[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs7023275	0.93[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7025669	0.81[CEU][hapmap]
rs7030846	0.81[EUR][1000 genomes]
rs7031365	0.83[EUR][1000 genomes]
rs7034484	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7035863	0.96[CEU][hapmap]
rs7036172	0.81[CEU][hapmap]
rs7036674	0.82[CEU][hapmap]
rs7036875	0.82[EUR][1000 genomes]
rs7042475	0.83[EUR][1000 genomes]
rs7046351	0.80[EUR][1000 genomes]
rs7389629	0.81[CEU][hapmap]
rs770524	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs7848511	0.81[EUR][1000 genomes]
rs7851056	0.83[EUR][1000 genomes]
rs7851323	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7856318	0.91[LWK][hapmap];0.80[YRI][hapmap]
rs7859780	0.81[CEU][hapmap]
rs7863088	0.81[CEU][hapmap]
rs7866629	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7873152	0.93[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7874533	0.80[CEU][hapmap]
rs7875367	0.84[ASW][hapmap];0.93[CEU][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9407624	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs954663	0.93[CEU][hapmap]
rs9650684	0.84[AMR][1000 genomes];0.91[EUR][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	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2457637	ADAMTSL1	cis	parietal	SCAN
rs2457637	C9orf93	cis	cerebellum	SCAN
rs2457637	C9orf93	cis	parietal	SCAN
rs2457637	C9orf93	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15530400-15533400	Enhancers	GM12878-XiMat	blood
2	chr9:15532400-15533400	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr9:15532600-15533400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:15532800-15533400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr9:15532800-15533400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr9:15532800-15533400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr9:15532800-15533400	Flanking Active TSS	Placenta	Placenta
8	chr9:15532800-15533400	Enhancers	Fetal Thymus	thymus
9	chr9:15533200-15533400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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