Variant report

Variant	rs2815074
Chromosome Location	chr6:39124008-39124009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39116542..39118295-chr6:39122485..39125265,2	K562	blood:
2	chr6:39082917..39084444-chr6:39122515..39124108,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112167	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1019772	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1155348	0.81[EUR][1000 genomes]
rs1366322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366324	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1366325	0.91[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1465570	0.94[GIH][hapmap];0.94[TSI][hapmap]
rs1544934	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1835004	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864061	0.81[EUR][1000 genomes]
rs1896681	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2162838	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs228819	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs2815056	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2815075	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815079	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2815088	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2815090	0.83[CEU][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs2815092	0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs57588867	0.91[AFR][1000 genomes]
rs61366612	0.91[AFR][1000 genomes]
rs9380834	0.84[EUR][1000 genomes]
rs962311	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2815074	C6orf64	cis	parietal	SCAN
rs2815074	C6orf64	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39122400-39125200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:39122400-39125800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:39122600-39125800	Weak transcription	Primary hematopoietic stem cells	blood

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