Variant report

Variant	rs9383573
Chromosome Location	chr6:150204205-150204206
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:

Variant related genes	Relation type
RAET1E-AS1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10457853	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17079029	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2342773	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4142628	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6557137	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6557163	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]
rs6904335	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6905778	0.90[EUR][1000 genomes]
rs6910351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6915465	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6927913	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6936944	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72997594	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7745070	0.89[EUR][1000 genomes]
rs7761734	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9322226	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9322227	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9322230	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9322231	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371216	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9371502	0.85[AMR][1000 genomes]
rs9371523	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9371555	0.90[EUR][1000 genomes]
rs9383569	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9383583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383916	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383942	0.89[EUR][1000 genomes]
rs9383943	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9383944	0.89[EUR][1000 genomes]
rs9383945	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9397049	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397053	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397057	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397060	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397071	0.90[EUR][1000 genomes]
rs9397387	0.85[AMR][1000 genomes]
rs9397394	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9397399	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397419	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397447	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397449	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9397451	0.83[CEU][hapmap];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9383573	RAET1E	cis	Esophagus Mucosa	GTEx

Chromatin state (count:5 , 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
5	chr6:150204200-150206800	Weak transcription	Hela-S3	cervix

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