Variant report

Variant	rs4961409
Chromosome Location	chr8:20770917-20770918
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	chr8:20767548..20769104-chr8:20769526..20772463,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10095438	0.84[ASN][1000 genomes]
rs10102368	0.81[ASN][1000 genomes]
rs10106561	0.84[ASN][1000 genomes]
rs1016650	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10503697	0.83[ASN][1000 genomes]
rs11776249	0.93[AMR][1000 genomes]
rs11782315	0.92[ASN][1000 genomes]
rs11990651	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1348196	0.82[ASN][1000 genomes]
rs1441783	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441784	0.86[ASN][1000 genomes]
rs1441786	1.00[CHB][hapmap]
rs17093328	0.84[ASN][1000 genomes]
rs17093344	0.93[ASN][1000 genomes]
rs17093353	0.87[ASN][1000 genomes]
rs17093359	0.87[ASN][1000 genomes]
rs17093371	0.87[ASN][1000 genomes]
rs17093374	0.85[ASN][1000 genomes]
rs17116662	0.90[ASN][1000 genomes]
rs17495275	0.92[CHB][hapmap]
rs2119697	0.91[ASN][1000 genomes]
rs2410671	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2410672	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28431990	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4961408	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4961413	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4961415	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4961417	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61382554	0.86[ASN][1000 genomes]
rs6586940	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6586942	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67522156	0.84[ASN][1000 genomes]
rs6988989	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7000262	0.80[JPT][hapmap]
rs7017108	0.93[ASN][1000 genomes]
rs7828057	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7840513	0.83[ASN][1000 genomes]
rs7840809	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7844603	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032450	chr8:20514995-21033577	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv539524	chr8:20514995-21033577	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1020160	chr8:20652610-20825810	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv539526	chr8:20652610-20825810	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1024612	chr8:20665835-20837761	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv539527	chr8:20665835-20837761	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv890646	chr8:20714686-20843176	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1034265	chr8:20742935-21152545	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv539528	chr8:20742935-21152545	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv890647	chr8:20749895-20847332	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv831258	chr8:20754932-20940380	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4961409	FGF20	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20765400-20774000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:20769800-20771800	Enhancers	Fetal Heart	heart
3	chr8:20770000-20771400	Enhancers	Left Ventricle	heart

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