Variant report

Variant	rs1956450
Chromosome Location	chr14:42081882-42081883
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	chr10:31677223..31678083-chr14:42081588..42082360,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10131184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10140527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs10149052	0.82[AMR][1000 genomes]
rs10483526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1103437	0.82[ASN][1000 genomes]
rs1111037	0.82[ASN][1000 genomes]
rs1111177	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1111179	0.92[CEU][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs11157240	0.81[EUR][1000 genomes]
rs11157241	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11157247	0.83[GIH][hapmap];0.96[MEX][hapmap]
rs1137567	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12431444	0.93[EUR][1000 genomes]
rs12437380	0.82[ASN][1000 genomes]
rs12879030	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1609735	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs17781288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1950831	0.95[EUR][1000 genomes]
rs1950834	0.93[EUR][1000 genomes]
rs1950835	0.92[CEU][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1950836	0.85[EUR][1000 genomes]
rs1950838	0.96[EUR][1000 genomes]
rs1956445	0.91[ASN][1000 genomes]
rs2121708	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4356390	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55897228	0.91[ASN][1000 genomes]
rs61990271	0.82[ASN][1000 genomes]
rs61990273	0.82[ASN][1000 genomes]
rs61990274	0.82[ASN][1000 genomes]
rs61990275	0.82[ASN][1000 genomes]
rs61990286	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990287	1.00[ASN][1000 genomes]
rs61990288	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990289	0.94[EUR][1000 genomes]
rs6572099	0.95[EUR][1000 genomes]
rs67505447	0.80[AMR][1000 genomes]
rs7148091	0.93[EUR][1000 genomes]
rs72684563	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8003822	0.95[EUR][1000 genomes]
rs8007172	0.94[EUR][1000 genomes]
rs8013655	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047300	chr14:41671653-42361098	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831164	chr14:41673017-42103168	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv533968	chr14:41882101-42327882	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1042078	chr14:41993985-42120143	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758353	chr14:42045873-42259511	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2759983	chr14:42045873-42259511	ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1956450	LRFN5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:42079800-42089800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:42080600-42085600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr14:42080800-42084200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:42080800-42084600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr14:42081000-42087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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