Variant report

Variant	rs2517911
Chromosome Location	chr6:29684634-29684635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29681737..29685555-chr6:29686615..29688782,3	MCF-7	breast:
2	chr6:29683436..29685775-chr6:29686962..29689399,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1419696	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1610588	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1610601	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1610602	0.80[ASN][1000 genomes]
rs1610612	0.80[ASN][1000 genomes]
rs1610621	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1610742	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1610744	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1628578	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1632957	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1632960	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1633096	0.80[ASN][1000 genomes]
rs1633098	0.80[ASN][1000 genomes]
rs1633099	0.80[ASN][1000 genomes]
rs1633106	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1633107	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1736915	0.80[ASN][1000 genomes]
rs2517910	0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3094730	0.87[EUR][1000 genomes]
rs3094731	0.87[EUR][1000 genomes]
rs3116799	0.81[EUR][1000 genomes]
rs3129046	0.86[EUR][1000 genomes]
rs3131864	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3131867	0.87[EUR][1000 genomes]
rs885942	0.80[ASN][1000 genomes]
rs885943	0.80[ASN][1000 genomes]
rs885944	0.80[ASN][1000 genomes]
rs885945	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs885946	0.81[ASN][1000 genomes]
rs9258068	0.85[EUR][1000 genomes]
rs929158	0.80[ASN][1000 genomes]
rs929159	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv2634641	chr6:29684594-29688509	Weak transcription Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2517911	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2517911	HLA-G	cis	lymphoblastoid	seeQTL
rs2517911	HIST1H3I	cis	cerebellum	SCAN
rs2517911	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2517911	ZKSCAN3	cis	parietal	SCAN
rs2517911	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2517911	HIST1H2BM	cis	cerebellum	SCAN
rs2517911	HLA-A	cis	lymphoblastoid	seeQTL
rs2517911	ZNF323	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29678400-29685200	Weak transcription	Esophagus	oesophagus
3	chr6:29678600-29689200	Weak transcription	GM12878-XiMat	blood
4	chr6:29681200-29688200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:29681800-29688200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:29682000-29688400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:29682400-29688200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:29684600-29684800	Flanking Bivalent TSS/Enh	Thymus	Thymus

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