Variant report

Variant	rs12619859
Chromosome Location	chr2:31416582-31416583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11124248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124249	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11124250	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124251	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124255	0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.87[ASN][1000 genomes]
rs11680892	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11681503	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11681673	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11687767	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11692905	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12619774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12623398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373218	0.88[ASN][1000 genomes]
rs1373219	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17011001	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs4952055	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4952068	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4952069	0.88[JPT][hapmap]
rs6543617	0.99[ASN][1000 genomes]
rs6731524	0.84[JPT][hapmap]
rs7585737	0.87[JPT][hapmap]
rs7591444	0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9789485	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv873771	chr2:31363732-31416582	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv873772	chr2:31363732-31417863	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv873773	chr2:31363732-31426449	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv873774	chr2:31363732-31432367	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873775	chr2:31363732-31439443	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873776	chr2:31384009-31439443	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv997652	chr2:31385242-31431588	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv535611	chr2:31385242-31431588	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12619859	AGBL5	cis	cerebellum	SCAN
rs12619859	GTF3C2	cis	parietal	SCAN
rs12619859	EHD3	cis	lymphoblastoid	seeQTL
rs12619859	EHD3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31391200-31418600	Weak transcription	Gastric	stomach
2	chr2:31394800-31419600	Weak transcription	Primary B cells from cord blood	blood
3	chr2:31395200-31416600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:31410800-31420400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:31411000-31421800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:31411000-31427400	Weak transcription	Fetal Brain Female	brain
7	chr2:31411200-31436800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:31412800-31416800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:31413200-31417400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:31413400-31425600	Weak transcription	Right Ventricle	heart
11	chr2:31415000-31418200	Strong transcription	Esophagus	oesophagus
12	chr2:31415400-31417000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:31415400-31417200	Enhancers	Fetal Intestine Large	intestine
14	chr2:31415400-31420800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:31416000-31416800	Enhancers	Fetal Intestine Small	intestine

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