Variant report

Variant	rs489951
Chromosome Location	chr7:100370800-100370801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:100370756..100373277-chr7:100392976..100395717,2	K562	blood:
2	chr7:100369436..100372255-chr7:100374074..100375616,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10226460	0.82[EUR][1000 genomes]
rs10232130	0.94[JPT][hapmap]
rs10247980	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs10953302	0.80[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs10953303	0.94[ASN][1000 genomes]
rs11772464	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs144173	0.85[CEU][hapmap]
rs1734903	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2075669	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs221804	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2230585	0.88[CEU][hapmap];0.88[GIH][hapmap]
rs2293767	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs3134668	0.92[EUR][1000 genomes]
rs314310	0.84[CEU][hapmap]
rs314343	0.80[EUR][1000 genomes]
rs314344	0.85[CEU][hapmap]
rs314353	0.85[CEU][hapmap]
rs314356	0.87[CEU][hapmap]
rs314358	0.85[CEU][hapmap]
rs314359	0.85[CEU][hapmap]
rs34361556	0.88[EUR][1000 genomes]
rs35253132	0.80[EUR][1000 genomes]
rs3891039	0.80[ASN][1000 genomes]
rs482308	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs484921	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs489830	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531503	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs539445	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs540330	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[LWK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs542137	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs559208	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs570087	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62483592	0.88[ASN][1000 genomes]
rs62483598	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62483599	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62483602	0.84[ASN][1000 genomes]
rs6942733	0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs6971700	0.86[CHD][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv888796	chr7:100313420-100423365	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs489951	MCM7	cis	cerebellum	SCAN
rs489951	VGF	cis	cerebellum	SCAN
rs489951	BUD31	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100358400-100381600	Weak transcription	Right Atrium	heart
2	chr7:100367800-100371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:100369600-100371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:100369800-100370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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