Variant report

Variant	rs1480157
Chromosome Location	chr5:146423429-146423430
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10059332	0.89[EUR][1000 genomes]
rs10067207	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10476881	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10477316	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875618	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs11167949	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11167951	0.93[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13362410	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1480158	0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2086375	0.89[EUR][1000 genomes]
rs2400232	0.88[EUR][1000 genomes]
rs2400235	0.93[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs28813131	0.89[EUR][1000 genomes]
rs4489112	0.93[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4552686	0.93[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705453	0.83[JPT][hapmap]
rs6876098	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72827248	0.91[ASN][1000 genomes]
rs72827252	0.91[ASN][1000 genomes]
rs72827261	0.82[ASN][1000 genomes]
rs9325028	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs9325030	0.86[CEU][hapmap];0.88[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	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1026599	chr5:146366481-146490089	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1480157	C5orf46	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146418800-146424200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:146421000-146424400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:146421000-146425000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:146421000-146425000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:146421400-146426800	Enhancers	Brain Cingulate Gyrus	brain
6	chr5:146421800-146427400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:146422200-146427000	Enhancers	Brain Anterior Caudate	brain
8	chr5:146422200-146428000	Enhancers	Brain Hippocampus Middle	brain
9	chr5:146422400-146423600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr5:146422400-146426800	Enhancers	Brain Angular Gyrus	brain
11	chr5:146422600-146429000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:146423000-146424200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:146423000-146425400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:146423200-146423600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:146423400-146428000	Enhancers	Brain Substantia Nigra	brain

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