Variant report

Variant	rs4741545
Chromosome Location	chr9:15830506-15830507
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 190 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs1009468	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs10732335	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10733301	0.83[AMR][1000 genomes]
rs10733302	0.86[AMR][1000 genomes]
rs10733305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10738411	0.86[AMR][1000 genomes]
rs10738413	0.82[ASN][1000 genomes]
rs10738415	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738417	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs10738419	0.86[CHB][hapmap]
rs10738420	0.85[CHB][hapmap]
rs10756687	0.91[MEX][hapmap]
rs10756688	0.82[MEX][hapmap]
rs10756696	0.85[AMR][1000 genomes]
rs10756697	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs10756704	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs10756709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10756710	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10756711	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10756713	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10756714	0.90[CHB][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10756715	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10756720	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[MKK][hapmap]
rs10756722	0.85[CHB][hapmap]
rs10756726	0.82[ASW][hapmap];0.86[CHB][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs10756728	0.86[CHB][hapmap];1.00[LWK][hapmap]
rs10756729	0.86[CHB][hapmap]
rs10810428	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs10810435	0.84[AMR][1000 genomes]
rs10810436	0.86[AMR][1000 genomes]
rs10810439	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs10810446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10810450	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10810452	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10810455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10810461	1.00[ASW][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap]
rs10810462	0.90[CHB][hapmap];0.81[AFR][1000 genomes]
rs10810483	0.85[CHB][hapmap]
rs10810484	0.85[CHB][hapmap];0.84[GIH][hapmap];0.96[MKK][hapmap]
rs10810485	0.85[CHB][hapmap]
rs10810486	0.90[CHB][hapmap]
rs10810487	0.90[CHB][hapmap]
rs10810488	0.82[ASW][hapmap];0.90[CHB][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs10810494	0.82[ASW][hapmap];0.95[MKK][hapmap]
rs10810501	0.86[CHB][hapmap]
rs10810502	0.86[CHB][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs10810506	0.86[CHB][hapmap]
rs10810509	0.82[ASW][hapmap];0.86[CHB][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs10962110	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10962142	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]
rs10962151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10962156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10962157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10962158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs10962167	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10962170	0.85[CEU][hapmap]
rs10962225	0.85[CHB][hapmap]
rs10962227	0.90[CHB][hapmap]
rs11515071	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11521158	0.80[ASN][1000 genomes]
rs11562188	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12057012	0.87[AMR][1000 genomes]
rs12378499	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12379234	0.84[CHB][hapmap]
rs12552653	0.84[AMR][1000 genomes]
rs12553816	0.81[AFR][1000 genomes];0.86[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]
rs13296360	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1341732	0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes]
rs1341737	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs1341738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1359952	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1396707	0.91[MEX][hapmap];0.80[TSI][hapmap]
rs1396708	1.00[ASW][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs1410444	0.85[CHB][hapmap]
rs1533040	0.91[MEX][hapmap]
rs1539172	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1539173	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1572978	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs1592099	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs1927696	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1927698	0.85[CHB][hapmap]
rs2105315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs2105317	0.90[JPT][hapmap]
rs2105318	0.87[AMR][1000 genomes]
rs2105319	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2153725	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs2153726	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs2153727	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs2175082	0.91[MEX][hapmap]
rs2185663	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2185665	0.81[JPT][hapmap]
rs2211323	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2225181	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2225182	0.86[CHB][hapmap]
rs2382540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2382553	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs2382554	0.81[AFR][1000 genomes]
rs2891007	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2987009	0.95[CHB][hapmap]
rs2987010	0.90[CHB][hapmap]
rs2987011	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs2987012	0.95[CHB][hapmap]
rs2987013	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs2987014	0.94[CHB][hapmap]
rs3008666	0.95[CHB][hapmap]
rs3008681	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs3008747	0.95[CHB][hapmap]
rs3008748	0.95[CHB][hapmap]
rs3008749	0.95[CHB][hapmap]
rs3008751	0.85[CHB][hapmap]
rs3008753	0.95[CHB][hapmap]
rs4146290	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4146291	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4146293	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4472620	0.85[CHB][hapmap]
rs4582646	0.85[CHB][hapmap]
rs4740619	0.87[MEX][hapmap]
rs4740624	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs4740627	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4740628	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4741528	0.82[MEX][hapmap]
rs4741534	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs4741535	1.00[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs4741546	0.82[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4741548	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4741552	0.82[ASW][hapmap];0.86[CHB][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs4741553	0.86[CHB][hapmap]
rs4961713	0.88[AMR][1000 genomes]
rs6474944	0.82[MEX][hapmap]
rs6474954	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs6474967	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6474974	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs7019205	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs7024640	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs7032457	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs7032634	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs7032755	0.87[MEX][hapmap]
rs7043770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7047045	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs735962	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7466716	0.80[ASN][1000 genomes]
rs7466717	0.88[AFR][1000 genomes]
rs769151	0.82[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs7846970	0.80[ASN][1000 genomes]
rs7847144	0.86[MEX][hapmap];0.80[TSI][hapmap]
rs7849380	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7853744	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs7857601	0.89[ASN][1000 genomes]
rs7860528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7860755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7860992	0.80[ASN][1000 genomes]
rs7866641	0.85[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs7866894	0.87[ASN][1000 genomes]
rs7873776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9298738	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs9298739	0.84[JPT][hapmap]
rs9298740	0.81[JPT][hapmap]
rs9298741	0.81[JPT][hapmap]
rs9406537	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9406542	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs9407648	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs9407649	0.81[JPT][hapmap]
rs9407650	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs9407651	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs9407652	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs9407654	0.85[CEU][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs9407657	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs9407661	0.81[JPT][hapmap]
rs9407662	0.81[JPT][hapmap]
rs950234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs955369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs961117	0.85[CHB][hapmap]
rs9650685	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9886731	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	nsv528964	chr9:15760822-15875162	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv892636	chr9:15794858-15876507	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv6486	chr9:15805220-15837639	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv508536	chr9:15811619-15834267	Enhancers Active TSS Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
10	esv1812927	chr9:15815363-15830506	Weak transcription Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
11	nsv613664	chr9:15815363-15830506	Weak transcription Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
12	nsv613666	chr9:15823667-15875162	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv613667	chr9:15823667-15876507	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4741545	C9orf93	cis	cerebellum	SCAN
rs4741545	C9orf93	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15814800-15831200	Weak transcription	Psoas Muscle	Psoas
2	chr9:15827000-15834600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:15830200-15857200	Weak transcription	Primary hematopoietic stem cells	blood

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