Variant report

Variant	rs7780625
Chromosome Location	chr7:38949938-38949939
allele	A/G
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	CTCF	chr7:38949820-38949970	GM12874	blood:	n/a	n/a

Variant related genes	Relation type
VPS41	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10247503	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10486677	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10486678	0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs11980882	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12670221	0.92[EUR][1000 genomes]
rs12672793	0.85[JPT][hapmap]
rs12672885	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12674115	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs1468348	0.80[JPT][hapmap]
rs17700142	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs17700172	0.80[JPT][hapmap]
rs17700262	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs17700752	0.85[CHD][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs17767818	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs17768153	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs17768711	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs17768753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2074655	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2074657	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs2108507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2189855	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs2240351	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2240352	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs2240353	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2286086	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs2286088	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2286098	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2286105	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs2286106	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2286109	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2392598	0.83[JPT][hapmap]
rs34724372	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs3801139	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs3801140	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs3801143	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs3801145	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs4723785	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs61363591	0.81[ASN][1000 genomes]
rs6462872	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6956146	0.91[EUR][1000 genomes]
rs6975048	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs733150	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs73357792	0.84[EUR][1000 genomes]
rs7780490	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7785911	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7795874	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7800167	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7803397	0.82[JPT][hapmap]
rs886646	0.88[JPT][hapmap]
rs9638944	0.81[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830967	chr7:38913837-39069253	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7780625	SEPT7	cis	cerebellum	SCAN
rs7780625	C7orf36	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38949000-38952000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:38949000-38952200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:38949000-38953000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38949200-38952200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:38949800-38950000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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