Variant report

Variant	rs9407649
Chromosome Location	chr9:15826603-15826604
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs1009468	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738415	0.96[ASN][1000 genomes]
rs10756686	0.83[CHB][hapmap]
rs10756687	0.84[CHB][hapmap]
rs10756688	0.89[CHB][hapmap]
rs10756689	0.89[CHB][hapmap]
rs10756690	0.84[CHB][hapmap]
rs10756704	0.81[JPT][hapmap]
rs10756710	0.82[JPT][hapmap]
rs10756711	0.82[JPT][hapmap]
rs10810427	0.84[CHB][hapmap]
rs10810428	0.84[CHB][hapmap]
rs10810429	0.83[CHB][hapmap]
rs10810438	0.94[CHB][hapmap]
rs10810440	0.88[CHB][hapmap]
rs10810442	1.00[CHB][hapmap]
rs1081245	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10962126	0.88[CHB][hapmap]
rs10962142	0.81[JPT][hapmap]
rs10962147	1.00[CHB][hapmap]
rs10962149	1.00[CHB][hapmap]
rs10962152	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs10962153	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs10962156	0.82[YRI][hapmap]
rs10962169	0.87[AMR][1000 genomes]
rs10962170	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10962171	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10962173	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11515218	0.83[AMR][1000 genomes]
rs11521158	0.83[AMR][1000 genomes]
rs1169478	0.84[CHB][hapmap]
rs1169479	0.94[CHB][hapmap]
rs1169480	0.89[CHB][hapmap]
rs12340969	0.83[CHB][hapmap]
rs12341679	0.88[CHB][hapmap]
rs12377371	0.89[CHB][hapmap]
rs12377532	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1328288	1.00[CHB][hapmap]
rs13296360	0.93[CEU][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1341734	1.00[CHB][hapmap]
rs1341737	0.92[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1341738	0.93[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1355171	0.84[CHB][hapmap]
rs1355173	1.00[CHB][hapmap]
rs1359953	0.89[CHB][hapmap]
rs1396706	0.88[CHB][hapmap]
rs1533040	0.84[CHB][hapmap]
rs1539171	1.00[CHB][hapmap]
rs1539172	0.81[JPT][hapmap]
rs1539173	0.82[YRI][hapmap]
rs1572978	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1578558	0.80[YRI][hapmap]
rs1592099	0.81[JPT][hapmap]
rs1891212	0.84[CHB][hapmap]
rs1984246	0.89[CHB][hapmap]
rs2066292	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2096121	1.00[CHB][hapmap]
rs2149231	0.89[CHB][hapmap]
rs2153725	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153726	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153727	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175082	0.83[CHB][hapmap]
rs2185665	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2382540	0.82[YRI][hapmap]
rs2382553	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2794634	1.00[CHB][hapmap]
rs2794636	1.00[CHB][hapmap]
rs2891007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2987069	0.89[CHB][hapmap]
rs2987070	1.00[CHB][hapmap]
rs2987071	1.00[CHB][hapmap]
rs2987072	1.00[CHB][hapmap]
rs3008686	1.00[CHB][hapmap]
rs35971661	0.84[AMR][1000 genomes]
rs4146291	0.81[JPT][hapmap]
rs4146293	0.93[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs451878	0.84[CHB][hapmap];0.83[YRI][hapmap]
rs4740619	0.82[CHB][hapmap]
rs4740624	0.81[JPT][hapmap]
rs4741528	0.89[CHB][hapmap]
rs4741534	0.82[CHB][hapmap]
rs4741545	0.81[JPT][hapmap]
rs4741546	0.86[JPT][hapmap]
rs56401042	0.82[AMR][1000 genomes]
rs6474944	0.82[CHB][hapmap]
rs6474945	0.83[CHB][hapmap]
rs6474954	0.82[CHB][hapmap]
rs6474966	0.94[CHB][hapmap]
rs6474967	0.81[JPT][hapmap]
rs7019205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7019851	1.00[CHB][hapmap]
rs7023275	0.84[CHB][hapmap]
rs7024440	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025669	0.89[CHB][hapmap]
rs7027202	0.89[CHB][hapmap]
rs7032457	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032634	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034484	0.87[CHB][hapmap]
rs7034781	0.94[CHB][hapmap]
rs7036674	0.87[CHB][hapmap]
rs7039881	0.84[YRI][hapmap]
rs7045018	1.00[CHB][hapmap]
rs7047045	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7388793	0.85[YRI][hapmap]
rs7467156	0.88[CHB][hapmap]
rs7467207	0.83[CHB][hapmap]
rs7470881	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs770191	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs770200	0.85[YRI][hapmap]
rs770201	0.85[YRI][hapmap]
rs770207	0.85[YRI][hapmap]
rs770211	1.00[CHB][hapmap]
rs770213	1.00[CHB][hapmap]
rs770215	0.89[CHB][hapmap]
rs7849380	0.93[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7853744	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857126	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857495	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7857601	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7860528	0.85[YRI][hapmap]
rs7860869	0.88[CHB][hapmap]
rs7866641	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7866894	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7869624	1.00[CHB][hapmap]
rs7871232	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7872912	1.00[CHB][hapmap]
rs9298738	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298740	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298741	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9406534	0.85[AMR][1000 genomes]
rs9406536	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9406537	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9406539	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9406540	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9406541	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9406542	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9406545	0.84[ASN][1000 genomes]
rs9407645	0.80[EUR][1000 genomes]
rs9407648	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407650	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9407651	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407652	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407653	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407654	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407655	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9407656	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9407657	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9407658	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9407659	0.83[AMR][1000 genomes]
rs9407660	0.91[ASN][1000 genomes]
rs9407661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs9407662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[ASN][1000 genomes]
rs9407669	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9407671	0.82[YRI][hapmap]
rs955369	0.81[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9407649	C9orf93	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15814800-15831200	Weak transcription	Psoas Muscle	Psoas
2	chr9:15826400-15827000	Enhancers	Brain Cingulate Gyrus	brain
3	chr9:15826400-15827000	Enhancers	Brain Hippocampus Middle	brain
4	chr9:15826600-15827000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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