Variant report

Variant	rs2056419
Chromosome Location	chr7:16132939-16132940
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1012401	0.83[AMR][1000 genomes]
rs1012402	0.80[AMR][1000 genomes]
rs1034958	0.83[ASN][1000 genomes]
rs1034959	0.93[CEU][hapmap]
rs10950599	0.83[AMR][1000 genomes]
rs11975989	0.93[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1295135	0.93[CEU][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1295136	0.93[CEU][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1295138	0.93[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs1295139	0.93[CEU][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1295142	0.93[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs1295143	0.93[CEU][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs13225542	0.83[ASN][1000 genomes]
rs13230369	0.85[AMR][1000 genomes]
rs1527196	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1527202	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1527204	0.85[AMR][1000 genomes]
rs1528137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1528148	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1918859	0.92[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1918860	0.84[AFR][1000 genomes]
rs2056420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4721472	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56064186	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6461221	0.85[AMR][1000 genomes]
rs6461225	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6945873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781532	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7798339	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs875127	0.86[ASN][1000 genomes]
rs969610	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv949309	chr7:15986709-16236162	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv949555	chr7:16078412-16279290	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2056419	TWIST1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16122200-16133000	Weak transcription	Psoas Muscle	Psoas
2	chr7:16122400-16135400	Weak transcription	Left Ventricle	heart
3	chr7:16131200-16133000	Enhancers	Fetal Lung	lung
4	chr7:16131600-16135400	Weak transcription	Fetal Stomach	stomach
5	chr7:16131800-16138000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:16132000-16135400	Weak transcription	Right Atrium	heart
7	chr7:16132000-16137400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:16132400-16137000	Weak transcription	HUVEC	blood vessel

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