Variant report

Variant	rs349541
Chromosome Location	chr3:140253779-140253780
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs168387	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16850427	0.81[CHD][hapmap]
rs180970	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs180971	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs189469	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs349535	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs349537	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs349538	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs349539	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs349565	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs349566	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs349567	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs349568	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs349570	1.00[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs349571	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs349572	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs479568	0.97[EUR][1000 genomes]
rs567167	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs571815	0.87[EUR][1000 genomes]
rs9832511	0.83[AMR][1000 genomes];0.83[EUR][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	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv591863	chr3:140126067-140274442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs349541	PIK3CB	cis	cerebellum	SCAN
rs349541	TFDP2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140248400-140254200	Weak transcription	Psoas Muscle	Psoas
2	chr3:140250000-140260400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:140252200-140253800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:140252200-140262600	Weak transcription	Adipose Nuclei	Adipose
5	chr3:140253000-140254200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:140253400-140263400	Weak transcription	Ovary	ovary
7	chr3:140253600-140254200	ZNF genes & repeats	HSMMtube	muscle

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