Variant report

Variant	rs10962142
Chromosome Location	chr9:15756094-15756095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 216 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:210)

rs_ID	r²[population]
rs1009468	0.81[JPT][hapmap]
rs10481557	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap]
rs10732335	0.82[AMR][1000 genomes]
rs10733301	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733302	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733305	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs10738405	0.80[EUR][1000 genomes]
rs10738406	0.80[EUR][1000 genomes]
rs10738411	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738413	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10738417	0.89[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs10756674	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs10756677	0.89[CEU][hapmap]
rs10756679	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10756686	0.85[CEU][hapmap]
rs10756687	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs10756688	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs10756689	0.89[CEU][hapmap]
rs10756690	0.89[CEU][hapmap]
rs10756692	0.90[AMR][1000 genomes]
rs10756695	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10756696	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756697	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756703	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756704	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10756709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10756710	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10756711	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10756714	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs10756715	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10756720	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10756722	0.85[CHB][hapmap]
rs10810399	0.89[CEU][hapmap]
rs10810401	0.89[CEU][hapmap]
rs10810402	0.85[CEU][hapmap]
rs10810408	0.89[CEU][hapmap];0.91[MEX][hapmap]
rs10810428	0.89[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs10810433	0.80[EUR][1000 genomes]
rs10810434	0.80[EUR][1000 genomes]
rs10810435	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10810436	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10810439	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810442	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10810450	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10810451	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10810452	0.81[AMR][1000 genomes]
rs10810455	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs10810461	0.84[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap]
rs10810462	0.90[CHB][hapmap]
rs10810483	0.85[CHB][hapmap]
rs10810484	0.85[CHB][hapmap];0.81[MKK][hapmap]
rs10810485	0.85[CHB][hapmap]
rs10810486	0.90[CHB][hapmap]
rs10810487	0.90[CHB][hapmap]
rs10810488	0.90[CHB][hapmap]
rs10810494	0.81[MKK][hapmap]
rs10810501	0.86[CHB][hapmap]
rs10810502	0.86[CHB][hapmap];0.81[MKK][hapmap]
rs10810506	0.86[CHB][hapmap]
rs10810509	0.86[CHB][hapmap];0.81[MKK][hapmap]
rs10962070	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs10962098	0.89[CEU][hapmap]
rs10962099	0.89[CEU][hapmap]
rs10962110	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10962124	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10962149	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10962151	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10962156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10962157	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10962158	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10962162	0.81[AMR][1000 genomes]
rs10962163	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10962167	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10962225	0.85[CHB][hapmap]
rs10962227	0.90[CHB][hapmap]
rs11515218	0.86[ASN][1000 genomes]
rs11521158	0.87[ASN][1000 genomes]
rs11562188	0.82[AMR][1000 genomes]
rs12057012	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12340969	0.85[CEU][hapmap]
rs12346205	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12349973	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12378499	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12379234	0.84[CHB][hapmap]
rs12552653	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12553816	0.96[AMR][1000 genomes]
rs1328283	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1328286	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs13287834	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13295778	0.81[ASN][1000 genomes]
rs13296276	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13296360	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1341732	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1341737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1341738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1359952	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1396707	0.85[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs1396708	0.84[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1410444	0.85[CHB][hapmap]
rs1509310	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1533040	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs1539172	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1539173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1553728	0.85[CEU][hapmap]
rs1572978	0.81[JPT][hapmap]
rs1592099	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1927696	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1927698	0.85[CHB][hapmap]
rs2055772	0.89[CEU][hapmap];0.91[MEX][hapmap]
rs2105315	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105317	0.81[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2105318	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2105319	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2136355	0.80[EUR][1000 genomes]
rs2153725	0.81[JPT][hapmap]
rs2153726	0.81[JPT][hapmap]
rs2153727	0.81[JPT][hapmap]
rs2175082	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs2185663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2185665	0.81[JPT][hapmap]
rs2211323	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2225181	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2225182	0.86[CHB][hapmap]
rs2382534	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs2382540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2382553	0.81[JPT][hapmap]
rs276435	0.81[CEU][hapmap]
rs2891002	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2891007	0.81[JPT][hapmap]
rs3008681	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs3119699	0.80[CEU][hapmap]
rs4146290	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4146291	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4146293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4472620	0.85[CHB][hapmap]
rs4582646	0.85[CHB][hapmap]
rs4740615	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs4740619	0.89[CEU][hapmap];0.91[MEX][hapmap]
rs4740624	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4740625	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4740627	0.82[AMR][1000 genomes]
rs4740628	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4741519	0.89[CEU][hapmap]
rs4741528	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs4741534	0.85[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs4741535	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4741542	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4741545	0.84[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.84[AMR][1000 genomes]
rs4741546	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap]
rs4741548	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4961713	0.83[AMR][1000 genomes]
rs6474931	0.88[CEU][hapmap]
rs6474944	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs6474945	0.89[CEU][hapmap]
rs6474953	0.80[EUR][1000 genomes]
rs6474954	0.85[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs6474955	0.80[EUR][1000 genomes]
rs6474966	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6474967	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6474974	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7024640	0.85[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7025669	0.89[CEU][hapmap]
rs7032634	0.81[JPT][hapmap]
rs7032755	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs7035863	0.81[CEU][hapmap]
rs7036172	0.89[CEU][hapmap]
rs7036674	0.91[CEU][hapmap]
rs7043770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7045018	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7047045	0.81[JPT][hapmap]
rs735962	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7389629	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7466716	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7466717	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs769151	0.81[MKK][hapmap]
rs7846970	0.88[ASN][1000 genomes]
rs7847144	0.85[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7849380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7853744	0.81[JPT][hapmap]
rs7855235	0.80[EUR][1000 genomes]
rs7859780	0.89[CEU][hapmap]
rs7860528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7860755	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7860992	0.88[ASN][1000 genomes]
rs7861802	0.92[ASN][1000 genomes]
rs7863088	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs7869624	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7873776	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7874533	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs9298738	0.81[JPT][hapmap]
rs9298739	0.84[JPT][hapmap]
rs9298740	0.81[JPT][hapmap]
rs9298741	0.81[JPT][hapmap]
rs9406537	0.81[JPT][hapmap]
rs9406542	0.81[JPT][hapmap]
rs9407648	0.81[JPT][hapmap]
rs9407649	0.81[JPT][hapmap]
rs9407650	0.81[JPT][hapmap]
rs9407651	0.81[JPT][hapmap]
rs9407652	0.81[JPT][hapmap]
rs9407654	0.81[JPT][hapmap]
rs9407657	0.81[JPT][hapmap]
rs9407661	0.81[JPT][hapmap]
rs9407662	0.81[JPT][hapmap]
rs950234	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955369	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs961117	0.85[CHB][hapmap]
rs9650685	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9886731	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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	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
2	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
3	esv2752286	chr9:15578017-15794897	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv892632	chr9:15590116-15869845	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv892633	chr9:15604746-15889411	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv892635	chr9:15731775-15876507	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10962142	C9orf93	cis	cerebellum	SCAN
rs10962142	C9orf93	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15742600-15769600	Weak transcription	Psoas Muscle	Psoas
2	chr9:15747200-15759600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:15748000-15757600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:15748000-15758000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:15755200-15756200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:15755200-15756200	Strong transcription	Primary hematopoietic stem cells	blood
7	chr9:15755800-15757400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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