Variant report

Variant	rs6582090
Chromosome Location	chr12:72893918-72893919
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10735969	0.94[CEU][hapmap]
rs10735970	0.88[EUR][1000 genomes]
rs10748198	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10748202	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs10748203	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs10784975	0.84[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs10784979	0.81[EUR][1000 genomes]
rs10879436	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879439	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10879461	0.81[EUR][1000 genomes]
rs10879462	0.81[EUR][1000 genomes]
rs11179226	0.82[ASN][1000 genomes]
rs11179228	0.95[CHD][hapmap]
rs11179240	0.91[CHD][hapmap]
rs11179280	0.81[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1214894	0.89[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1214897	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1214899	0.84[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1347194	0.81[EUR][1000 genomes]
rs1347196	0.81[EUR][1000 genomes]
rs1353160	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1389497	0.93[CEU][hapmap];0.83[CHB][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1444606	0.94[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1444607	0.94[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1687265	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1817885	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1836042	0.81[EUR][1000 genomes]
rs1836043	0.81[EUR][1000 genomes]
rs1836044	0.80[EUR][1000 genomes]
rs1864837	0.81[EUR][1000 genomes]
rs1864838	0.81[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs1899907	0.84[CHD][hapmap]
rs1965318	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2130660	0.82[CHB][hapmap]
rs2367747	0.85[EUR][1000 genomes]
rs2887071	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3782362	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs3782366	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3782367	0.83[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817612	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3843025	0.81[EUR][1000 genomes]
rs3852549	0.81[GIH][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs3852550	0.81[EUR][1000 genomes]
rs3910234	0.82[EUR][1000 genomes]
rs4100196	0.82[EUR][1000 genomes]
rs605027	0.87[CEU][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs626266	0.84[CHD][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6582094	0.81[EUR][1000 genomes]
rs6582095	0.81[EUR][1000 genomes]
rs683101	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131984	0.93[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs7135547	0.81[EUR][1000 genomes]
rs71457035	0.81[EUR][1000 genomes]
rs723867	0.94[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7295506	0.93[CHD][hapmap]
rs7299984	0.81[EUR][1000 genomes]
rs7308678	0.85[EUR][1000 genomes]
rs7309263	0.81[GIH][hapmap]
rs7309330	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs7309651	0.81[EUR][1000 genomes]
rs7310174	0.81[CHB][hapmap]
rs7311350	0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs7967001	0.87[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7969680	0.81[EUR][1000 genomes]
rs7969934	0.81[EUR][1000 genomes]
rs954147	0.84[CHD][hapmap]
rs963407	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs996575	0.86[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv832453	chr12:72778058-72966827	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv817280	chr12:72820558-73508605	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv899259	chr12:72885554-73011367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6582090	RAB3IP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72880600-72901600	Weak transcription	Pancreas	Pancrea
2	chr12:72880600-72905600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:72890400-72902000	Weak transcription	Fetal Intestine Small	intestine
4	chr12:72892000-72897600	Weak transcription	Right Atrium	heart
5	chr12:72892400-72901600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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