Variant report

Variant	rs13165556
Chromosome Location	chr5:146433478-146433479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10077240	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs10077327	0.87[EUR][1000 genomes]
rs1031915	0.83[CEU][hapmap];0.89[GIH][hapmap]
rs1031916	0.83[CEU][hapmap];0.89[GIH][hapmap]
rs11167956	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1125457	0.83[CEU][hapmap]
rs11743368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12523317	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13183391	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1383167	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs1383168	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs1480154	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054528	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2400241	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6880660	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6880992	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs6881673	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs720303	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720305	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs922585	0.86[GIH][hapmap]
rs9325031	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs9325032	1.00[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs997979	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv2757142	chr5:146429843-146539500	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2759385	chr5:146429843-146539500	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146426000-146434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:146426400-146434200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:146426400-146435600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:146431800-146434600	Enhancers	Brain Substantia Nigra	brain
5	chr5:146432000-146433800	Enhancers	Brain Hippocampus Middle	brain
6	chr5:146433200-146433600	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr5:146433200-146434400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:146433200-146434400	Enhancers	Brain Anterior Caudate	brain
9	chr5:146433400-146433600	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr5:146433400-146434000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:146433400-146434200	Active TSS	Brain Inferior Temporal Lobe	brain

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