Variant report

Variant	rs606407
Chromosome Location	chr3:101609650-101609651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1672376	0.87[ASN][1000 genomes]
rs1672379	0.89[ASN][1000 genomes]
rs1672382	0.91[ASN][1000 genomes]
rs1672384	0.91[ASN][1000 genomes]
rs1707600	0.82[ASN][1000 genomes]
rs1707610	0.84[ASN][1000 genomes]
rs2925329	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2942717	0.82[ASN][1000 genomes]
rs635268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs771572	1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs796417	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs797867	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic 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	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic 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	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1010762	chr3:101584836-101803821	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3436195	chr3:101608162-101612460	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs606407	RG9MTD1	cis	parietal	SCAN
rs606407	ABI3BP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101607800-101614600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:101608000-101609800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:101608000-101611000	Weak transcription	Aorta	Aorta
4	chr3:101609000-101609800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:101609000-101609800	Enhancers	NH-A	brain
6	chr3:101609200-101610000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:101609200-101610400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:101609200-101611000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:101609400-101609800	Enhancers	Osteobl	bone
10	chr3:101609600-101609800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:101609600-101609800	Enhancers	Liver	Liver
12	chr3:101609600-101609800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr3:101609600-101610000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:101609600-101610200	Enhancers	HUVEC	blood vessel
15	chr3:101609600-101611000	Weak transcription	Primary monocytes fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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