Variant report

Variant	rs17400427
Chromosome Location	chr15:49741071-49741072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49740094..49742331-chr15:49762242..49764123,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1023683	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519221	1.00[ASN][1000 genomes]
rs10519226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519227	0.89[AFR][1000 genomes]
rs11630318	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11632038	1.00[ASN][1000 genomes]
rs11632303	1.00[ASN][1000 genomes]
rs11632575	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11633282	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11634636	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11635005	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11635308	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635354	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638314	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638606	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11639423	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592277	0.84[AFR][1000 genomes]
rs12913966	1.00[ASN][1000 genomes]
rs1354918	0.81[AMR][1000 genomes]
rs1588127	0.81[AMR][1000 genomes]
rs17396119	1.00[ASN][1000 genomes]
rs17396536	1.00[ASN][1000 genomes]
rs17396747	1.00[ASN][1000 genomes]
rs17397211	1.00[ASN][1000 genomes]
rs17400706	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17400916	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476361	1.00[ASN][1000 genomes]
rs17477722	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17477923	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17478618	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479003	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479205	0.89[AFR][1000 genomes]
rs17479289	0.89[AFR][1000 genomes]
rs17480434	0.81[AMR][1000 genomes]
rs28393768	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408092	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28409376	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28430272	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465200	0.81[AMR][1000 genomes]
rs28484276	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28492008	0.81[AMR][1000 genomes]
rs28635979	0.81[AMR][1000 genomes]
rs28669217	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35692325	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4338740	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57252806	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57749497	1.00[ASN][1000 genomes]
rs59112977	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60594237	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61259878	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162633	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7165168	1.00[ASN][1000 genomes]
rs7167474	1.00[ASN][1000 genomes]
rs7168316	0.89[AFR][1000 genomes]
rs73392236	1.00[ASN][1000 genomes]
rs73392249	1.00[ASN][1000 genomes]
rs73392256	1.00[ASN][1000 genomes]
rs73392277	1.00[ASN][1000 genomes]
rs73392288	1.00[ASN][1000 genomes]
rs73394324	1.00[ASN][1000 genomes]
rs73394333	1.00[ASN][1000 genomes]
rs73394339	1.00[ASN][1000 genomes]
rs73394355	1.00[ASN][1000 genomes]
rs73394359	1.00[ASN][1000 genomes]
rs73396235	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73396238	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73398223	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73398243	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398264	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73398272	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398276	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73398284	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400205	0.86[AFR][1000 genomes]
rs8027094	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030457	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040716	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv9263	chr15:49734435-49809465	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv526246	chr15:49738233-49749735	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17400427	FGF7	cis	Muscle Skeletal	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49730400-49744600	Weak transcription	NHLF	lung
2	chr15:49732000-49750200	Weak transcription	HSMM	muscle
3	chr15:49733200-49741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:49737000-49741800	Weak transcription	Osteobl	bone
5	chr15:49737000-49751200	Weak transcription	Ovary	ovary
6	chr15:49737600-49744200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:49739200-49744200	Weak transcription	NHDF-Ad	bronchial
8	chr15:49739600-49741600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:49739800-49741200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:49740400-49741200	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:49740600-49741200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:49740800-49741600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:49741000-49742800	Enhancers	Fetal Heart	heart
14	chr15:49741000-49743200	Enhancers	Rectal Smooth Muscle	rectum

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