Variant report

Variant	rs9462007
Chromosome Location	chr6:34715341-34715342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11756392	1.00[CEU][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759235	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555773	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894959	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883638	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997775	0.84[YRI][hapmap]
rs2395607	0.81[ASW][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492859	0.80[EUR][1000 genomes]
rs2744937	0.90[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs2744942	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2744947	0.84[EUR][1000 genomes]
rs2744954	1.00[CEU][hapmap]
rs2744955	1.00[CEU][hapmap]
rs2744956	1.00[CEU][hapmap]
rs2744964	0.90[CEU][hapmap]
rs2744971	1.00[CEU][hapmap]
rs2744972	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[EUR][1000 genomes]
rs2744977	0.90[CEU][hapmap]
rs2764203	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764204	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2764205	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814943	0.90[CEU][hapmap];0.89[GIH][hapmap]
rs2814944	0.90[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs2814948	0.89[EUR][1000 genomes]
rs2814960	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814962	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814983	0.90[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs2814985	0.90[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs2814993	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs2814994	1.00[CEU][hapmap]
rs2814996	1.00[CEU][hapmap]
rs2815005	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[EUR][1000 genomes]
rs28567450	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736896	0.81[AFR][1000 genomes]
rs3800457	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[EUR][1000 genomes]
rs4472337	0.84[EUR][1000 genomes]
rs4646925	0.89[GIH][hapmap]
rs56693020	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56930444	0.83[EUR][1000 genomes]
rs59142559	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60643641	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61431557	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457790	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911549	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936177	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6938239	0.92[EUR][1000 genomes]
rs73419607	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73419621	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755822	0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762485	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847854	0.84[YRI][hapmap]
rs847855	0.84[YRI][hapmap]
rs9296130	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296140	0.84[YRI][hapmap]
rs9462012	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9462014	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9462016	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462025	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462029	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469860	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469864	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469890	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469895	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469897	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469900	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469907	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469910	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469911	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469913	0.87[EUR][1000 genomes]
rs9469919	0.88[YRI][hapmap]
rs9469926	0.82[YRI][hapmap]
rs9654581	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688715	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv885795	chr6:34704613-34823187	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv870010	chr6:34713359-34880048	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9462007	C6orf106	cis	parietal	SCAN
rs9462007	C6orf107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34711600-34715400	Enhancers	Fetal Intestine Large	intestine
2	chr6:34713400-34715600	Enhancers	K562	blood
3	chr6:34713600-34716200	Enhancers	Stomach Mucosa	stomach
4	chr6:34714400-34715800	Weak transcription	Esophagus	oesophagus
5	chr6:34714400-34716200	Enhancers	HepG2	liver
6	chr6:34715200-34715400	Enhancers	Small Intestine	intestine

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