Variant report

Variant	rs6494978
Chromosome Location	chr15:33518480-33518481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11858945	1.00[CHD][hapmap]
rs12900513	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12903983	0.83[EUR][1000 genomes]
rs12907653	1.00[CHB][hapmap]
rs12908986	0.83[EUR][1000 genomes]
rs12910017	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910336	1.00[CHB][hapmap];0.87[GIH][hapmap]
rs4328408	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780093	0.83[EUR][1000 genomes]
rs6494977	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7179324	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7179886	0.83[EUR][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	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv482299	chr15:33449137-33624122	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv533346	chr15:33469439-33809641	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv832963	chr15:33514798-33712442	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6494978	TJP1	cis	cerebellum	SCAN
rs6494978	OCA2	cis	cerebellum	SCAN
rs6494978	ARHGAP11B	cis	parietal	SCAN
rs6494978	MTMR10	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33517800-33518800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:33517800-33518800	Enhancers	Primary T cells from cord blood	blood
3	chr15:33517800-33519000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr15:33517800-33519000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:33517800-33519200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:33517800-33519200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr15:33517800-33519400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr15:33517800-33519400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr15:33517800-33519400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr15:33517800-33519400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:33517800-33519400	Enhancers	Dnd41	blood
12	chr15:33518000-33518800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr15:33518000-33519000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:33518000-33519200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr15:33518000-33519200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:33518000-33519200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr15:33518000-33519200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:33518000-33519200	Enhancers	Fetal Thymus	thymus
19	chr15:33518200-33518600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:33518200-33518800	Enhancers	Primary hematopoietic stem cells	blood
21	chr15:33518200-33518800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr15:33518200-33519200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:33518200-33519200	Enhancers	Thymus	Thymus
24	chr15:33518400-33518800	Enhancers	Skeletal Muscle Female	skeletal muscle

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