Variant report

Variant	rs4870078
Chromosome Location	chr6:150201812-150201813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:150200786-150205208	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150201367..150203467-chr6:150207974..150210289,2	MCF-7	breast:

Variant related genes	Relation type
RAET1E-AS1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10457852	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204653	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12209310	1.00[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12210822	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12527391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528243	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1855572	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999632	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1999633	0.88[CEU][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2342766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798763	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3922946	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3922947	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4869755	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4869756	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4869767	0.94[CEU][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4869768	0.94[CEU][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4870117	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4870118	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5024811	0.94[CEU][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57894361	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6557165	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6912330	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6925151	1.00[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7452592	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7764677	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs915140	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9322229	1.00[CEU][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9371228	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9383941	1.00[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9397070	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4870078	RAET1G	cis	Thyroid	GTEx
rs4870078	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs4870078	SHPRH	cis	cerebellum	SCAN
rs4870078	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs4870078	LATS1	cis	cerebellum	SCAN
rs4870078	RP11-350J20.5	cis	lung	GTEx
rs4870078	NUP43	cis	multi-tissue	Pritchard
rs4870078	LATS1	cis	parietal	SCAN
rs4870078	LRP11	cis	cerebellum	SCAN
rs4870078	LRP11	cis	parietal	SCAN
rs4870078	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150198000-150205200	Weak transcription	Esophagus	oesophagus
2	chr6:150201400-150202600	Enhancers	Ovary	ovary

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