Variant report

Variant	rs1007415
Chromosome Location	chr14:39399093-39399094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10134739	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12883114	0.85[CHB][hapmap]
rs12885731	0.83[ASN][1000 genomes]
rs17616347	0.85[CHB][hapmap]
rs1884383	0.85[CHB][hapmap]
rs1885143	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1950508	0.85[CHB][hapmap]
rs1951226	0.88[ASN][1000 genomes]
rs2025060	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2025062	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2144527	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs35976812	0.83[ASN][1000 genomes]
rs6571879	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6571880	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7140282	0.85[CHB][hapmap]
rs743222	0.81[ASN][1000 genomes]
rs7493678	0.88[ASN][1000 genomes]
rs8007240	0.85[CHB][hapmap]
rs8020013	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8020321	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv564416	chr14:39140536-39440106	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv470631	chr14:39153764-39440106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv932194	chr14:39173578-39411337	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv901656	chr14:39370726-39423339	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1007415	SEC23A	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39397400-39401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:39398400-39400200	Enhancers	Brain Substantia Nigra	brain
3	chr14:39398400-39400400	Enhancers	Brain Cingulate Gyrus	brain
4	chr14:39398600-39399600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr14:39398800-39399800	Enhancers	Brain Angular Gyrus	brain
6	chr14:39398800-39400000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:39398800-39400800	Enhancers	Brain Hippocampus Middle	brain

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