Variant report

Variant	rs6508729
Chromosome Location	chr19:37985809-37985810
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37985665..37987976-chr19:37996433..37998090,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188227	Chromatin interaction
ENSG00000266916	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1038085	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10425671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11672077	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs11883392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1236810	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs1465434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1530500	1.00[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs1871197	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2045909	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2160640	0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2199644	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs256737	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs256739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2617789	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2972456	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4803228	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs6508738	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7251097	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs7254170	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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 lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6508729	ITPKC	cis	cerebellum	SCAN
rs6508729	EXOSC5	cis	cerebellum	SCAN
rs6508729	IGFL4	cis	parietal	SCAN
rs6508729	CATSPERG	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37984800-37988200	Weak transcription	Brain Substantia Nigra	brain
2	chr19:37984800-37988200	Weak transcription	Fetal Brain Male	brain
3	chr19:37984800-37996400	Weak transcription	Fetal Heart	heart

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