Variant report

Variant	rs10266560
Chromosome Location	chr7:70765291-70765292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10226199	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10231965	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10256635	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs10261998	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10263619	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272997	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11976781	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12155368	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12668780	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs12669285	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12673556	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs1465231	0.88[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1558003	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1574440	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs1922527	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2141885	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs2527289	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs2527297	0.87[CEU][hapmap];0.84[JPT][hapmap]
rs2527298	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs2527312	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs28631036	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28670821	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867411	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28799658	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3923571	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073529	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4446620	0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6460649	0.91[EUR][1000 genomes]
rs67615560	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6942815	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943983	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6961808	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6976562	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6976574	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6976591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73177835	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73179792	0.88[EUR][1000 genomes]
rs73356099	0.86[EUR][1000 genomes]
rs7778324	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs7792223	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9638618	0.88[GIH][hapmap]
rs9690269	0.83[ASN][1000 genomes]
rs9886302	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10266560	STAG3L4	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70751200-70768200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:70751800-70768600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:70751800-70768800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:70752200-70773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:70760400-70765400	Weak transcription	Fetal Stomach	stomach
6	chr7:70764000-70768800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:70764200-70765600	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:70764800-70765400	Weak transcription	Left Ventricle	heart
9	chr7:70765000-70765800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr7:70765000-70766000	Enhancers	Fetal Muscle Trunk	muscle
11	chr7:70765000-70766200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:70765000-70766200	Enhancers	Fetal Muscle Leg	muscle
13	chr7:70765000-70775400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:70765200-70765400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:70765200-70765600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:70765200-70765600	Enhancers	Ovary	ovary
17	chr7:70765200-70765800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:70765200-70765800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr7:70765200-70765800	Enhancers	Fetal Heart	heart
20	chr7:70765200-70765800	Enhancers	Fetal Lung	lung
21	chr7:70765200-70765800	Enhancers	HSMMtube	muscle
22	chr7:70765200-70766000	Enhancers	HepG2	liver

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