Variant report

Variant	rs11917714
Chromosome Location	chr3:119533346-119533347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119531732..119533815-chr3:119534255..119536418,2	MCF-7	breast:
2	chr3:119532575..119535119-chr3:119538231..119540719,2	K562	blood:
3	chr3:119532575..119536291-chr3:119538231..119540719,3	K562	blood:
4	chr3:119533302..119535583-chr3:119535890..119538879,2	MCF-7	breast:
5	chr3:119531331..119533784-chr3:119534969..119537956,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10433404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10934500	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10934502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes]
rs10934503	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11915717	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12054090	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12108149	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12629015	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634476	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12634889	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12638973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13314595	0.82[YRI][hapmap]
rs1574154	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16830567	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1719889	0.89[YRI][hapmap]
rs1980718	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276707	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2873950	0.80[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28831519	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3732359	0.83[JPT][hapmap];0.86[TSI][hapmap]
rs3732360	0.83[JPT][hapmap]
rs3732361	0.87[JPT][hapmap]
rs3814057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4340737	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4624596	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688042	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688046	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688047	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4688054	0.80[ASN][1000 genomes]
rs56728675	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57939147	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58493895	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60389731	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60393216	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62264706	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264708	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264714	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264734	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62264739	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62264742	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62264743	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62264747	0.80[ASN][1000 genomes]
rs6773751	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6782799	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs6784598	0.87[JPT][hapmap]
rs6790751	0.82[YRI][hapmap]
rs6797459	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6808874	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7617372	0.82[YRI][hapmap]
rs7620750	0.82[YRI][hapmap]
rs7633279	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11917714	FBXO40	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119516800-119534600	Weak transcription	HepG2	liver
2	chr3:119528200-119533800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:119529400-119533600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:119529400-119533600	Weak transcription	Colonic Mucosa	Colon
5	chr3:119529400-119535800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:119529400-119537000	Strong transcription	Fetal Intestine Large	intestine
7	chr3:119529400-119537800	Strong transcription	Fetal Intestine Small	intestine
8	chr3:119529400-119544000	Weak transcription	Right Atrium	heart
9	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:119529600-119536000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:119529600-119543400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
13	chr3:119529800-119543600	Weak transcription	GM12878-XiMat	blood
14	chr3:119530200-119542800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:119531400-119534600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:119531600-119536200	Weak transcription	Fetal Heart	heart
17	chr3:119532000-119543800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:119532200-119533600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:119532400-119535800	Weak transcription	Left Ventricle	heart
20	chr3:119532400-119551000	Weak transcription	Right Ventricle	heart
21	chr3:119533200-119534400	Genic enhancers	Liver	Liver

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