Variant report

Variant	rs6474957
Chromosome Location	chr9:15735854-15735855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10119257	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10119980	0.91[EUR][1000 genomes]
rs10121391	0.90[EUR][1000 genomes]
rs10217374	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1039812	0.97[EUR][1000 genomes]
rs1039815	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1039816	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1041529	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs10429512	0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs10732334	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10733296	0.97[EUR][1000 genomes]
rs10738407	1.00[EUR][1000 genomes]
rs10756706	0.90[EUR][1000 genomes]
rs10810445	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810447	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10962061	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12006236	0.84[ASW][hapmap]
rs12350267	0.97[EUR][1000 genomes]
rs1355172	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1417974	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1417975	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1472941	1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1509311	0.91[EUR][1000 genomes]
rs1553727	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1848583	0.91[EUR][1000 genomes]
rs1891208	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1935225	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1964706	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1970496	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs202321	0.90[EUR][1000 genomes]
rs2055773	0.97[EUR][1000 genomes]
rs2055774	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2089618	1.00[EUR][1000 genomes]
rs2136354	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2136357	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2175083	0.97[EUR][1000 genomes]
rs2185664	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2221706	0.87[EUR][1000 genomes]
rs2382531	0.90[EUR][1000 genomes]
rs2382533	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2382535	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2382536	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs276434	0.83[GIH][hapmap]
rs276440	0.90[EUR][1000 genomes]
rs276442	0.90[EUR][1000 genomes]
rs3122701	0.84[EUR][1000 genomes]
rs3122705	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs381205	0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs398117	0.91[EUR][1000 genomes]
rs398178	0.90[EUR][1000 genomes]
rs401393	0.90[EUR][1000 genomes]
rs4146289	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4146292	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4237140	0.91[EUR][1000 genomes]
rs443563	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4445326	0.91[EUR][1000 genomes]
rs4740623	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4741532	0.90[EUR][1000 genomes]
rs4741533	0.90[EUR][1000 genomes]
rs4741536	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4741537	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4741540	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6474941	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6474947	0.90[EUR][1000 genomes]
rs6474949	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6474956	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6474961	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6474973	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6474977	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7025247	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7035422	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7037893	0.85[EUR][1000 genomes]
rs7038920	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7468716	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7847148	0.94[EUR][1000 genomes]
rs7849159	0.97[EUR][1000 genomes]
rs7859685	0.86[EUR][1000 genomes]
rs7860339	0.83[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs7865193	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7865391	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7866413	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7870315	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7874094	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs811282	0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9298734	0.90[EUR][1000 genomes]
rs955193	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs958870	0.86[ASW][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9919009	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv892634	chr9:15696501-15746168	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv32957	chr9:15720059-15737099	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6474957	C9orf93	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15679800-15746800	Weak transcription	Ovary	ovary
2	chr9:15687600-15746600	Weak transcription	Aorta	Aorta
3	chr9:15715200-15746200	Weak transcription	Left Ventricle	heart
4	chr9:15718000-15749600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:15718600-15746600	Weak transcription	Thymus	Thymus
6	chr9:15729000-15746800	Weak transcription	Fetal Thymus	thymus
7	chr9:15733200-15739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:15734600-15736000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:15734600-15736800	Enhancers	Osteobl	bone
10	chr9:15734800-15736000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:15734800-15736000	Enhancers	Fetal Heart	heart
12	chr9:15734800-15736000	Enhancers	HSMM	muscle
13	chr9:15734800-15736000	Enhancers	NH-A	brain
14	chr9:15734800-15736200	Enhancers	A549	lung
15	chr9:15734800-15736200	Enhancers	HUVEC	blood vessel
16	chr9:15734800-15736200	Enhancers	NHDF-Ad	bronchial
17	chr9:15734800-15736200	Enhancers	NHEK	skin
18	chr9:15734800-15736400	Enhancers	HMEC	breast
19	chr9:15734800-15736600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:15734800-15736600	Enhancers	Hela-S3	cervix
21	chr9:15734800-15737000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:15734800-15738400	Enhancers	Fetal Lung	lung
23	chr9:15735200-15736400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:15735400-15736000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr9:15735400-15738000	Weak transcription	HSMMtube	muscle
26	chr9:15735600-15736200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:15735600-15736200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:15735600-15736200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:15735600-15736600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:15735800-15736000	Flanking Active TSS	NHLF	lung
31	chr9:15735800-15737400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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