Variant report

Variant	rs246743
Chromosome Location	chr7:140690009-140690010
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140682579..140684839-chr7:140688833..140690514,2	MCF-7	breast:
2	chr7:140401092..140402939-chr7:140689274..140690916,2	K562	blood:
3	chr7:140688813..140691144-chr7:140711832..140714766,2	K562	blood:
4	chr7:140689349..140691695-chr7:140694980..140697473,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090266	Chromatin interaction
ENSG00000090263	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10243698	0.81[EUR][1000 genomes]
rs10244762	0.81[ASW][hapmap]
rs10271387	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279193	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1089265	0.92[EUR][1000 genomes]
rs1091374	1.00[ASN][1000 genomes]
rs1091557	0.92[EUR][1000 genomes]
rs12534351	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534354	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860481	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079829	1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246738	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246740	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246741	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246742	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246744	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246745	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs246746	0.92[EUR][1000 genomes]
rs2533300	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2533307	1.00[ASN][1000 genomes]
rs2533308	1.00[ASN][1000 genomes]
rs2688429	1.00[ASN][1000 genomes]
rs3844322	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38716	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38725	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38727	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38728	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38729	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38733	0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs38737	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38741	0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs38743	0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4020017	1.00[ASN][1000 genomes]
rs4020018	1.00[ASN][1000 genomes]
rs4726134	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4726136	0.85[EUR][1000 genomes]
rs62486599	0.88[EUR][1000 genomes]
rs6949856	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950813	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71645926	1.00[ASN][1000 genomes]
rs7778860	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782666	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787917	0.90[EUR][1000 genomes]
rs801096	1.00[ASN][1000 genomes]
rs801097	1.00[ASN][1000 genomes]
rs801118	0.92[EUR][1000 genomes]
rs801119	0.90[EUR][1000 genomes]
rs801122	0.88[EUR][1000 genomes]
rs801124	0.92[EUR][1000 genomes]
rs801126	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs9640306	0.92[EUR][1000 genomes];1.00[ASN][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	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs246743	MRPS33	cis	cerebellum	SCAN
rs246743	MRPS33	cis	parietal	SCAN
rs246743	EPHA1	cis	cerebellum	SCAN
rs246743	SVOPL	cis	cerebellum	SCAN
rs246743	TMEM178B	cis	Esophagus Mucosa	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140687400-140691400	Enhancers	Fetal Intestine Small	intestine
2	chr7:140688400-140691200	Enhancers	Fetal Intestine Large	intestine
3	chr7:140689200-140693000	Enhancers	HepG2	liver
4	chr7:140689800-140690400	Enhancers	Duodenum Mucosa	Duodenum
5	chr7:140690000-140690200	Enhancers	Stomach Mucosa	stomach

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