Variant report

Variant	rs3930809
Chromosome Location	chr13:29738328-29738329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1111373	0.87[CHB][hapmap]
rs11147364	0.85[JPT][hapmap]
rs11618923	0.85[JPT][hapmap]
rs1335655	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs1577477	0.83[CHB][hapmap]
rs1927830	0.87[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs4495979	0.85[JPT][hapmap]
rs4559776	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4769687	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs4769691	0.89[CHB][hapmap]
rs5010846	0.82[ASN][1000 genomes]
rs6490360	0.85[JPT][hapmap]
rs7330035	0.85[JPT][hapmap]
rs7997258	0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8000236	0.82[ASN][1000 genomes]
rs9506114	0.85[JPT][hapmap]
rs9508299	0.85[JPT][hapmap]
rs9508300	0.85[JPT][hapmap]
rs9508302	0.85[JPT][hapmap]
rs9508311	0.83[CHB][hapmap]
rs9551608	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs9551615	0.83[CHB][hapmap]
rs9579301	0.81[ASN][1000 genomes]
rs9579304	0.87[CHB][hapmap]
rs989845	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs989846	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][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	nsv533835	chr13:29141132-29962069	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3406145	chr13:29616606-29917459	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899957	chr13:29720732-29820422	Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv455851	chr13:29728058-29746494	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv561391	chr13:29728058-29746494	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv427927	chr13:29729315-30062054	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3930809	SLC46A3	cis	cerebellum	SCAN
rs3930809	GTF3A	cis	cerebellum	SCAN
rs3930809	COL8A2	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:29734400-29752600	Weak transcription	Aorta	Aorta
2	chr13:29735400-29739200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr13:29736000-29739600	Weak transcription	Fetal Heart	heart
4	chr13:29737000-29739400	Weak transcription	GM12878-XiMat	blood
5	chr13:29738200-29738600	Enhancers	Fetal Stomach	stomach

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