Variant report

Variant	rs1453066
Chromosome Location	chr4:86179423-86179424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11097049	0.81[EUR][1000 genomes]
rs11728060	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11728312	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736900	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939907	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11940969	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11941989	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11946273	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12502364	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106310	0.90[ASN][1000 genomes]
rs13142921	0.94[ASN][1000 genomes]
rs1453065	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453067	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453068	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597897	0.81[EUR][1000 genomes]
rs1996355	0.92[ASN][1000 genomes]
rs2869278	0.95[ASN][1000 genomes]
rs2869282	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2869283	0.84[CHB][hapmap]
rs34782257	0.95[ASN][1000 genomes]
rs35297898	0.95[ASN][1000 genomes]
rs4280720	0.95[ASN][1000 genomes]
rs4373153	0.95[ASN][1000 genomes]
rs55875958	0.95[ASN][1000 genomes]
rs61190955	0.95[ASN][1000 genomes]
rs6531795	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531796	0.95[ASN][1000 genomes]
rs6531798	0.95[ASN][1000 genomes]
rs6531814	0.83[EUR][1000 genomes]
rs6823334	0.95[ASN][1000 genomes]
rs6826532	0.95[ASN][1000 genomes]
rs6830662	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838954	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853645	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855573	0.95[ASN][1000 genomes]
rs6857037	0.91[ASN][1000 genomes]
rs715751	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7663029	0.95[ASN][1000 genomes]
rs7666306	0.95[ASN][1000 genomes]
rs7668499	0.93[ASN][1000 genomes]
rs7668722	0.95[ASN][1000 genomes]
rs7671100	0.95[ASN][1000 genomes]
rs7673737	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7674448	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7675311	0.95[ASN][1000 genomes]
rs7684110	0.84[ASN][1000 genomes]
rs7684365	0.89[ASN][1000 genomes]
rs7685564	0.95[ASN][1000 genomes]
rs7685722	0.95[ASN][1000 genomes]
rs7685988	0.95[ASN][1000 genomes]
rs7688124	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7688707	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689227	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7694080	0.95[ASN][1000 genomes]
rs7695625	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3367963	chr4:85911017-86246036	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	nsv427685	chr4:86032872-86340548	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1453066	EIF1	trans	cerebellum	SCAN
rs1453066	FSCB	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86178600-86179600	Enhancers	Fetal Intestine Small	intestine
2	chr4:86179200-86179600	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr4:86179400-86180600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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