Variant report

Variant	rs879667
Chromosome Location	chr6:35779879-35779880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10484264	0.81[GIH][hapmap]
rs1049649	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs10947572	0.82[CEU][hapmap]
rs1160828	0.85[CEU][hapmap]
rs11755072	0.85[CEU][hapmap]
rs1326752	0.85[CEU][hapmap]
rs17653835	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs17705020	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2038961	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2051647	0.85[CEU][hapmap]
rs2301510	0.85[CEU][hapmap]
rs2395640	0.85[CEU][hapmap]
rs2766522	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2766527	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2766528	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2817019	0.86[EUR][1000 genomes]
rs2817027	0.82[CEU][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2859420	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3213580	0.86[CEU][hapmap]
rs3761981	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3891863	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs4340986	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs4713929	0.86[EUR][1000 genomes]
rs612262	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs638600	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs639421	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs6457858	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs6457862	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs651158	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs662713	0.82[CEU][hapmap]
rs677937	0.85[CEU][hapmap]
rs6908433	0.85[CEU][hapmap]
rs6909895	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6910260	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6911849	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6916941	0.91[CEU][hapmap]
rs6920616	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6920862	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6923015	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs6929493	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6931888	0.82[CEU][hapmap]
rs6932973	0.85[CEU][hapmap]
rs6933241	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7740886	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs7752545	0.85[CEU][hapmap]
rs7752551	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs7755022	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7755600	0.85[CEU][hapmap]
rs7758042	0.83[GIH][hapmap]
rs879493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879668	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9296168	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs9462128	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs9462132	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9462134	0.85[CEU][hapmap]
rs9462135	0.85[CEU][hapmap]
rs9462136	0.83[GIH][hapmap]
rs9462141	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9462143	0.85[CEU][hapmap]
rs9470120	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470121	0.85[CEU][hapmap]
rs9470126	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470131	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470134	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9470138	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470139	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470141	0.85[CEU][hapmap]
rs9470144	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470147	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs9470152	0.85[CEU][hapmap]
rs9470153	0.85[CEU][hapmap]
rs9470154	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470155	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs9470156	0.84[CEU][hapmap]
rs9470162	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470171	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9470172	0.85[CEU][hapmap];0.81[GIH][hapmap]

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	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
6	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv885805	chr6:35685955-35779879	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	esv1791730	chr6:35754783-35805144	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv602939	chr6:35758072-35783497	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs879667	C6orf106	cis	cerebellum	SCAN
rs879667	CDKN1A	cis	cerebellum	SCAN
rs879667	BRPF3	cis	cerebellum	SCAN
rs879667	SRPK1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35773000-35791400	Weak transcription	Right Atrium	heart
2	chr6:35776200-35785000	Weak transcription	Brain Anterior Caudate	brain
3	chr6:35777000-35782400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:35777000-35801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:35778600-35780200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:35778600-35780400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:35778800-35780400	Enhancers	Esophagus	oesophagus
8	chr6:35779600-35780000	Enhancers	A549	lung
9	chr6:35779600-35782200	Weak transcription	Pancreas	Pancrea
10	chr6:35779800-35780400	Enhancers	Hela-S3	cervix

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