Variant report

Variant	rs2252229
Chromosome Location	chr3:100631579-100631580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10049238	1.00[JPT][hapmap]
rs1036468	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10511180	1.00[JPT][hapmap]
rs12330346	1.00[JPT][hapmap]
rs1375510	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1449321	1.00[JPT][hapmap]
rs17338729	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs17339226	0.88[CHB][hapmap]
rs17398137	1.00[JPT][hapmap]
rs1821795	1.00[JPT][hapmap]
rs1836985	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2245370	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs2304513	1.00[JPT][hapmap]
rs2576367	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2576370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2576381	0.81[EUR][1000 genomes]
rs2576384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576389	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576390	0.81[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2595899	0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2713749	0.88[CHB][hapmap]
rs2713750	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2713759	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2713762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs2713782	0.86[YRI][hapmap]
rs2713794	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28605965	0.92[ASN][1000 genomes]
rs6774218	0.88[CHB][hapmap]
rs73143029	1.00[ASN][1000 genomes]
rs7355920	1.00[JPT][hapmap]
rs7426715	0.80[EUR][1000 genomes]
rs7609734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7625454	0.88[CHB][hapmap]
rs7641631	0.88[CHB][hapmap]
rs7646218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
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:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
rs2252229	TFG	cis	cerebellum	SCAN
rs2252229	ABI3BP	cis	Artery Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:100612200-100632200	Weak transcription	Fetal Stomach	stomach
3	chr3:100617600-100641000	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:100617800-100641000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:100621600-100633400	Weak transcription	HSMMtube	muscle
6	chr3:100622000-100631800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:100623200-100631800	Weak transcription	NHDF-Ad	bronchial
8	chr3:100629800-100631800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:100630200-100634200	Weak transcription	NHLF	lung
10	chr3:100630200-100673600	Weak transcription	Ovary	ovary
11	chr3:100630400-100631800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:100630400-100631800	Weak transcription	Osteobl	bone
13	chr3:100630400-100647000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:100630600-100631600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:100631000-100633400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:100631400-100632200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr3:100631400-100632400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:100631400-100632400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:100631400-100632400	Enhancers	HSMM	muscle

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