Variant report

Variant	rs339731
Chromosome Location	chr3:42767359-42767360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10490794	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10865922	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11129975	0.83[EUR][1000 genomes]
rs11129976	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11129977	0.82[EUR][1000 genomes]
rs11718476	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11922251	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11922832	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11929390	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12054446	0.82[ASN][1000 genomes]
rs12487729	0.91[ASN][1000 genomes]
rs12491179	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633707	0.92[ASN][1000 genomes]
rs12635736	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12639142	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13070029	0.85[EUR][1000 genomes]
rs13070345	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13096498	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1975927	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs2240859	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2372110	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs339670	1.00[YRI][hapmap]
rs339671	0.89[EUR][1000 genomes]
rs339684	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34549959	0.89[ASN][1000 genomes]
rs34868846	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35584330	0.88[EUR][1000 genomes]
rs3843369	0.90[EUR][1000 genomes]
rs3846063	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3895740	0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3907218	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3912104	0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3916334	0.91[ASN][1000 genomes]
rs4683332	0.91[CEU][hapmap];0.81[GIH][hapmap];0.88[EUR][1000 genomes]
rs4683335	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs60706321	0.83[ASN][1000 genomes]
rs6442067	0.88[EUR][1000 genomes]
rs6779561	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6807878	0.86[ASN][1000 genomes]
rs7629781	1.00[YRI][hapmap]
rs7639170	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7639483	0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7641046	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs9830553	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9839430	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs339731	CCDC13	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42760400-42769600	Weak transcription	Right Atrium	heart
2	chr3:42760400-42773600	Enhancers	Brain Substantia Nigra	brain
3	chr3:42761200-42768600	Weak transcription	Left Ventricle	heart
4	chr3:42762800-42768000	Enhancers	Brain Hippocampus Middle	brain
5	chr3:42763600-42773600	Enhancers	Brain Anterior Caudate	brain
6	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
7	chr3:42763800-42771400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:42764000-42771000	Weak transcription	Psoas Muscle	Psoas
9	chr3:42764800-42768000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:42765000-42769000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42765000-42771000	Weak transcription	Right Ventricle	heart
12	chr3:42765000-42772600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:42765200-42770800	Weak transcription	Fetal Heart	heart
14	chr3:42766000-42768600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:42766400-42768000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:42766600-42768000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:42766800-42767600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:42766800-42767800	Weak transcription	Brain Cingulate Gyrus	brain

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