Variant report

Variant	rs1316575
Chromosome Location	chr6:54165300-54165301
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	chr6:54164489..54166885-chr6:54172521..54174692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137251	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1058768	0.87[GIH][hapmap]
rs11751405	0.88[EUR][1000 genomes]
rs1340670	0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs1353708	0.85[JPT][hapmap]
rs1396380	0.88[EUR][1000 genomes]
rs1508633	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1605674	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17574067	0.88[EUR][1000 genomes]
rs1995768	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs2136136	0.88[EUR][1000 genomes]
rs2153536	0.88[EUR][1000 genomes]
rs2153537	0.88[EUR][1000 genomes]
rs2185506	0.88[EUR][1000 genomes]
rs2297981	0.89[AMR][1000 genomes]
rs2397156	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2840308	0.88[EUR][1000 genomes]
rs3756808	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777651	0.81[JPT][hapmap]
rs3777652	0.85[JPT][hapmap]
rs4142450	0.88[EUR][1000 genomes]
rs4415156	0.91[EUR][1000 genomes]
rs4712061	1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62396368	0.88[EUR][1000 genomes]
rs6458990	0.88[EUR][1000 genomes]
rs7763301	0.88[EUR][1000 genomes]
rs7763740	0.88[EUR][1000 genomes]
rs7767969	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7769117	0.89[EUR][1000 genomes]
rs7771868	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7775058	0.88[EUR][1000 genomes]
rs9349702	0.88[EUR][1000 genomes]
rs9367562	0.85[JPT][hapmap]
rs9370282	0.88[EUR][1000 genomes]
rs9370283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395931	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs991287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2762594	chr6:54159146-54168766	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1316575	HCRTR2	cis	parietal	SCAN
rs1316575	TINAG	Cis_1M	lymphoblastoid	RTeQTL
rs1316575	TINAG	cis	parietal	SCAN
rs1316575	GSTA1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54164600-54165400	Enhancers	NHLF	lung
2	chr6:54164600-54166200	Enhancers	NHDF-Ad	bronchial
3	chr6:54164800-54166800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:54165200-54165400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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