Variant report

Variant	rs2595899
Chromosome Location	chr3:100698454-100698455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10049238	1.00[JPT][hapmap]
rs1036468	0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs10511180	1.00[JPT][hapmap]
rs12330346	1.00[JPT][hapmap]
rs1375510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17338729	1.00[JPT][hapmap]
rs17398137	1.00[JPT][hapmap]
rs1821795	1.00[JPT][hapmap]
rs1836985	0.88[CEU][hapmap]
rs2245370	0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2252229	0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2304513	1.00[JPT][hapmap]
rs2576367	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576370	0.81[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2576384	0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2576389	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2576390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713747	0.83[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713750	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713759	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2713762	0.81[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7355920	1.00[JPT][hapmap]
rs7609734	1.00[JPT][hapmap]
rs7632416	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646218	1.00[JPT][hapmap]
rs7647099	1.00[JPT][hapmap]
rs7651634	1.00[JPT][hapmap]
rs9653904	1.00[JPT][hapmap]
rs9822089	1.00[JPT][hapmap]
rs9824648	1.00[JPT][hapmap]
rs9825288	1.00[JPT][hapmap]
rs9826284	1.00[JPT][hapmap]
rs9827075	1.00[JPT][hapmap]
rs9827694	1.00[JPT][hapmap]
rs9831620	1.00[JPT][hapmap]
rs9843102	1.00[JPT][hapmap]
rs9844950	1.00[JPT][hapmap]
rs9847485	1.00[JPT][hapmap]
rs9860250	1.00[JPT][hapmap]
rs9862373	1.00[JPT][hapmap]
rs9866199	1.00[JPT][hapmap]
rs9881388	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2595899	ABI3BP	cis	Artery Tibial	GTEx
rs2595899	TFG	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100688400-100701800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:100692000-100700200	Weak transcription	HSMM	muscle
3	chr3:100692200-100701400	Weak transcription	Fetal Lung	lung
4	chr3:100692600-100711200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:100693000-100700400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:100694800-100700000	Weak transcription	Ovary	ovary
7	chr3:100696200-100702200	Enhancers	Fetal Stomach	stomach
8	chr3:100697000-100698800	Enhancers	Osteobl	bone
9	chr3:100697400-100698600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:100697600-100698600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr3:100697800-100699600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:100698000-100699600	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:100698000-100699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:100698000-100699800	Weak transcription	HSMMtube	muscle
15	chr3:100698000-100700000	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:100698000-100700000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:100698000-100701600	Weak transcription	Psoas Muscle	Psoas
18	chr3:100698200-100699800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:100698200-100699800	Weak transcription	NHDF-Ad	bronchial
20	chr3:100698400-100701400	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links