Variant report

Variant	rs12885731
Chromosome Location	chr14:39433803-39433804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1007415	0.83[ASN][1000 genomes]
rs10134739	0.82[ASN][1000 genomes]
rs1028591	0.84[ASN][1000 genomes]
rs1040836	0.84[ASN][1000 genomes]
rs12883114	0.86[CHB][hapmap]
rs12883946	0.84[ASN][1000 genomes]
rs12887605	0.84[ASN][1000 genomes]
rs12895569	0.86[ASN][1000 genomes]
rs17607605	0.84[ASN][1000 genomes]
rs17616347	0.86[CHB][hapmap]
rs17670531	0.84[ASN][1000 genomes]
rs17676972	0.86[ASN][1000 genomes]
rs1884383	0.86[CHB][hapmap]
rs1885143	0.82[ASN][1000 genomes]
rs1950508	0.86[CHB][hapmap]
rs1960796	0.84[ASN][1000 genomes]
rs2025060	0.90[ASN][1000 genomes]
rs2025062	0.90[ASN][1000 genomes]
rs2144526	0.82[ASN][1000 genomes]
rs2144527	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs34292075	0.84[ASN][1000 genomes]
rs35873738	0.84[ASN][1000 genomes]
rs61338087	0.84[ASN][1000 genomes]
rs6571879	0.82[ASN][1000 genomes]
rs6571880	0.82[ASN][1000 genomes]
rs7140282	0.86[CHB][hapmap]
rs7143056	0.84[ASN][1000 genomes]
rs7143370	0.85[ASN][1000 genomes]
rs7151407	0.86[ASN][1000 genomes]
rs7154223	0.86[ASN][1000 genomes]
rs8007240	0.86[CHB][hapmap]
rs8020013	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs8020321	0.86[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	nsv901657	chr14:39410706-39460072	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12885731	SEC23A	cis	parietal	SCAN
rs12885731	MIA2	cis	parietal	SCAN
rs12885731	TRAPPC6B	cis	cerebellum	SCAN
rs12885731	CTAGE5	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39428600-39435400	Weak transcription	Left Ventricle	heart
2	chr14:39429000-39434000	Weak transcription	Brain Anterior Caudate	brain
3	chr14:39433400-39434400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr14:39433400-39434600	Enhancers	HepG2	liver
5	chr14:39433600-39434000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:39433600-39434000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr14:39433600-39434000	Enhancers	Brain Angular Gyrus	brain
8	chr14:39433600-39434000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr14:39433600-39434000	Enhancers	Fetal Kidney	kidney
10	chr14:39433600-39434000	Enhancers	HSMM	muscle
11	chr14:39433600-39434200	Enhancers	Brain Substantia Nigra	brain
12	chr14:39433600-39434200	Enhancers	NH-A	brain
13	chr14:39433600-39434400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:39433800-39434000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr14:39433800-39434000	Enhancers	Fetal Stomach	stomach
16	chr14:39433800-39434200	Enhancers	A549	lung

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