Variant report

Variant	rs12527391
Chromosome Location	chr6:150203292-150203293
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	chr6:150198184..150200903-chr6:150202024..150204310,2	K562	blood:
2	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: 7 )

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

rs_ID	r²[population]
rs10457852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204653	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12209310	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12210822	0.96[AMR][1000 genomes];0.94[EUR][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	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1999633	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[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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4869756	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4869767	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4869768	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4870078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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[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	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6912330	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6925151	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	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9371228	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9383941	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12527391	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs12527391	RAET1G	cis	Thyroid	GTEx
rs12527391	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs12527391	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs12527391	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs12527391	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs12527391	RP11-350J20.5	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150198000-150205200	Weak transcription	Esophagus	oesophagus
2	chr6:150202600-150205200	Weak transcription	Right Atrium	heart
3	chr6:150202600-150205400	Weak transcription	Ovary	ovary
4	chr6:150202800-150208600	Weak transcription	HSMMtube	muscle

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