Variant report

Variant	rs6474967
Chromosome Location	chr9:15760988-15760989
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 213 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:206)

rs_ID	r²[population]
rs1009468	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs10217681	1.00[YRI][hapmap]
rs1039815	1.00[YRI][hapmap]
rs1039816	1.00[YRI][hapmap]
rs10429512	0.91[LWK][hapmap]
rs10481557	0.95[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs10733295	0.80[TSI][hapmap]
rs10733301	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10733302	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10733305	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10738411	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738413	0.87[ASN][1000 genomes]
rs10738417	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10738419	0.86[CHB][hapmap]
rs10756679	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10756696	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10756697	0.84[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10756703	0.84[ASN][1000 genomes]
rs10756704	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[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	0.90[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]
rs10756726	0.86[CHB][hapmap]
rs10810435	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10810436	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10810438	0.80[EUR][1000 genomes]
rs10810439	0.84[ASW][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10810440	0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs10810446	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10810450	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10810451	0.86[ASN][1000 genomes]
rs10810455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10810461	0.84[ASW][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10810462	0.90[CHB][hapmap]
rs10810483	0.85[CHB][hapmap]
rs10810484	0.85[CHB][hapmap]
rs10810485	0.85[CHB][hapmap]
rs10810486	0.90[CHB][hapmap]
rs10810487	0.90[CHB][hapmap]
rs10810488	0.90[CHB][hapmap]
rs10810501	0.86[CHB][hapmap]
rs10810502	0.86[CHB][hapmap]
rs10810506	0.86[CHB][hapmap]
rs10810509	0.86[CHB][hapmap]
rs10962110	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10962126	0.86[MEX][hapmap];0.80[TSI][hapmap]
rs10962142	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]
rs10962146	0.86[EUR][1000 genomes]
rs10962147	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs10962151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10962152	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10962153	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs10962156	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10962157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10962158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10962163	0.87[ASN][1000 genomes]
rs10962167	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10962225	0.85[CHB][hapmap]
rs10962227	0.90[CHB][hapmap]
rs11515218	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11521158	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12057012	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12341679	0.91[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs12346205	0.80[ASN][1000 genomes]
rs12349973	0.85[ASN][1000 genomes]
rs12377371	0.80[EUR][1000 genomes]
rs12378499	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12379234	0.84[CHB][hapmap]
rs12552653	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12553816	0.86[AMR][1000 genomes]
rs1328283	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1328286	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs13283620	0.89[EUR][1000 genomes]
rs13287834	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13295778	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13296276	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13296360	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs1341732	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1341734	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1341735	0.83[AMR][1000 genomes]
rs1341737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1341738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1355171	0.82[TSI][hapmap]
rs1355173	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1359952	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1396706	0.82[CEU][hapmap]
rs1396708	0.84[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap]
rs1410444	0.85[CHB][hapmap]
rs1417974	1.00[YRI][hapmap]
rs1417975	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs1539171	0.89[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1539172	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539173	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1572978	0.81[JPT][hapmap]
rs1592099	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1927696	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1927698	0.85[CHB][hapmap]
rs1935225	1.00[YRI][hapmap]
rs1970497	0.89[EUR][1000 genomes]
rs2096121	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2105315	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2105317	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2105318	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2105319	0.84[ASN][1000 genomes]
rs2136354	1.00[YRI][hapmap]
rs2153725	0.81[JPT][hapmap]
rs2153726	0.81[JPT][hapmap]
rs2153727	0.81[JPT][hapmap]
rs2175080	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2185663	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2185665	0.81[JPT][hapmap]
rs2211323	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2225181	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2225182	0.86[CHB][hapmap]
rs2382540	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2382553	0.81[JPT][hapmap]
rs2891007	0.81[JPT][hapmap]
rs3008681	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs34700988	0.88[EUR][1000 genomes]
rs36013000	0.90[EUR][1000 genomes]
rs4146290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4146291	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4146293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4472620	0.85[CHB][hapmap]
rs451878	0.80[TSI][hapmap]
rs4582646	0.85[CHB][hapmap]
rs4740623	1.00[YRI][hapmap]
rs4740624	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4740625	0.82[ASN][1000 genomes]
rs4740628	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4741535	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4741536	1.00[YRI][hapmap]
rs4741537	1.00[YRI][hapmap]
rs4741542	0.88[ASN][1000 genomes]
rs4741545	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4741546	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4741548	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4741552	0.86[CHB][hapmap]
rs56401042	0.85[AMR][1000 genomes]
rs58517712	0.89[EUR][1000 genomes]
rs62571268	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6474952	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs6474962	0.87[EUR][1000 genomes]
rs6474963	0.88[EUR][1000 genomes]
rs6474964	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6474965	0.88[EUR][1000 genomes]
rs6474974	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs7018872	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7019143	0.89[EUR][1000 genomes]
rs7019205	0.82[MEX][hapmap]
rs7019323	0.89[EUR][1000 genomes]
rs7019851	0.85[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7023275	0.91[MEX][hapmap]
rs7025420	0.89[EUR][1000 genomes]
rs7032634	0.81[JPT][hapmap]
rs7034781	0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs7035422	0.85[YRI][hapmap]
rs7036775	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7043770	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7047045	0.81[JPT][hapmap]
rs735962	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7389629	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7466716	0.89[ASN][1000 genomes]
rs7466717	0.83[ASN][1000 genomes]
rs7467207	0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7846970	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7849380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7853744	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs7857601	0.81[AMR][1000 genomes]
rs7860024	0.85[EUR][1000 genomes]
rs7860528	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7860755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7860992	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7861802	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7866413	1.00[YRI][hapmap]
rs7866641	0.86[MEX][hapmap]
rs7866894	0.80[ASN][1000 genomes]
rs7869624	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7872912	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7873776	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7875367	0.91[MEX][hapmap]
rs9298738	0.81[JPT][hapmap]
rs9298739	0.83[JPT][hapmap]
rs9298740	0.81[JPT][hapmap]
rs9298741	0.81[JPT][hapmap]
rs9406537	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs9406542	0.80[JPT][hapmap]
rs9407648	0.81[JPT][hapmap]
rs9407649	0.81[JPT][hapmap]
rs9407650	0.81[JPT][hapmap]
rs9407651	0.81[JPT][hapmap]
rs9407652	0.80[JPT][hapmap]
rs9407654	0.81[JPT][hapmap]
rs9407657	0.81[JPT][hapmap]
rs9407661	0.81[JPT][hapmap]
rs9407662	0.81[JPT][hapmap]
rs950234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs955193	0.86[LWK][hapmap]
rs955369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs961117	0.85[CHB][hapmap]
rs9650685	0.81[ASN][1000 genomes]
rs9886731	0.83[AMR][1000 genomes];0.88[ASN][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	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
7	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6474967	C9orf93	cis	cerebellum	SCAN
rs6474967	FREM1	cis	cerebellum	SCAN
rs6474967	C9orf93	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15742600-15769600	Weak transcription	Psoas Muscle	Psoas
2	chr9:15756200-15790800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:15757800-15763200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:15759200-15784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:15760800-15761400	Enhancers	Fetal Heart	heart

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