Variant report

Variant	rs1147721
Chromosome Location	chr3:120214270-120214271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1123897	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1147719	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1147720	0.83[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs11713908	0.94[ASN][1000 genomes]
rs1259311	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1259314	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259318	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1259320	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1259321	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1259322	0.87[ASN][1000 genomes]
rs1259329	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1259334	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1259336	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1259337	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1259338	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1267675	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1270209	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs1716835	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1733319	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs2252084	0.85[JPT][hapmap]
rs2319821	0.91[ASN][1000 genomes]
rs34182414	0.96[ASN][1000 genomes]
rs3914889	0.94[ASN][1000 genomes]
rs4408894	0.92[ASN][1000 genomes]
rs4676792	0.96[ASN][1000 genomes]
rs4676793	0.96[ASN][1000 genomes]
rs5029440	0.92[ASN][1000 genomes]
rs55662337	0.91[ASN][1000 genomes]
rs55854851	0.96[ASN][1000 genomes]
rs61797633	0.90[ASN][1000 genomes]
rs61797634	0.90[ASN][1000 genomes]
rs6438582	0.86[ASN][1000 genomes]
rs6438583	0.88[ASN][1000 genomes]
rs6777371	0.88[ASN][1000 genomes]
rs8180105	0.93[ASN][1000 genomes]
rs8180108	0.96[ASN][1000 genomes]
rs874477	0.91[JPT][hapmap]
rs9631455	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs9857229	0.96[ASN][1000 genomes]
rs9870449	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1147721	ARGFX	cis	parietal	SCAN
rs1147721	FSTL1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120206000-120216800	Weak transcription	Aorta	Aorta
2	chr3:120207000-120215000	Weak transcription	Osteobl	bone
3	chr3:120207200-120214600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:120212600-120214400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:120213600-120217200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:120214200-120215000	ZNF genes & repeats	HSMM	muscle
7	chr3:120214200-120215200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:120214200-120215400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:120214200-120215400	Enhancers	NHDF-Ad	bronchial

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