Variant report

Variant	rs6905778
Chromosome Location	chr6:150235933-150235934
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150215963..150217672-chr6:150235749..150238672,2	K562	blood:
2	chr6:150235746..150238768-chr6:150240556..150244338,4	MCF-7	breast:
3	chr6:150232168..150236512-chr6:150243000..150246593,4	K562	blood:

Variant related genes	Relation type
ENSG00000203722	Chromatin interaction
ENSG00000164520	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10457853	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17079029	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2342773	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4142628	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6557137	0.88[EUR][1000 genomes]
rs6557163	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6904335	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910351	0.90[EUR][1000 genomes]
rs6915465	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927913	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6936944	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72997594	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7745070	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7761734	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9322226	0.88[EUR][1000 genomes]
rs9322227	0.88[EUR][1000 genomes]
rs9322230	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9322231	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9371216	0.88[EUR][1000 genomes]
rs9371523	0.92[EUR][1000 genomes]
rs9371539	0.90[EUR][1000 genomes]
rs9371555	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383569	0.88[EUR][1000 genomes]
rs9383573	0.90[EUR][1000 genomes]
rs9383583	0.92[EUR][1000 genomes]
rs9383916	0.90[EUR][1000 genomes]
rs9383942	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383943	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383944	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9383945	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9397049	0.88[EUR][1000 genomes]
rs9397053	0.88[EUR][1000 genomes]
rs9397056	0.91[EUR][1000 genomes]
rs9397057	0.90[EUR][1000 genomes]
rs9397060	0.90[EUR][1000 genomes]
rs9397071	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9397394	0.88[EUR][1000 genomes]
rs9397399	0.90[EUR][1000 genomes]
rs9397419	0.90[EUR][1000 genomes]
rs9397447	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9397449	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9397451	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv970172	chr6:150235248-150244455	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6905778	RAET1E	cis	Nerve Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150226200-150242000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:150227800-150243400	Weak transcription	Right Ventricle	heart
3	chr6:150230200-150239000	Weak transcription	Esophagus	oesophagus
4	chr6:150230400-150243600	Weak transcription	Pancreas	Pancrea
5	chr6:150231600-150239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:150235400-150238400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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