Variant report

Variant	rs72738949
Chromosome Location	chr15:50668999-50669000
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50656520..50659033-chr15:50667252..50669894,2	K562	blood:
2	chr15:50665109..50666861-chr15:50668510..50670054,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1056681	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070770	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11855995	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12440601	0.82[EUR][1000 genomes]
rs12903381	0.82[EUR][1000 genomes]
rs12917303	0.80[EUR][1000 genomes]
rs17509458	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2013885	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2013888	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2414049	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4775879	0.84[AMR][1000 genomes]
rs504781	0.81[EUR][1000 genomes]
rs6493439	0.86[EUR][1000 genomes]
rs677143	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72738935	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv524613	chr15:50656449-50868779	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs72738949	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs72738949	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs72738949	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs72738949	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs72738949	CTD-3110H11.1	cis	lung	GTEx
rs72738949	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs72738949	GABPB1-AS1	cis	Heart Left Ventricle	GTEx
rs72738949	GABPB1-AS1	cis	Thyroid	GTEx
rs72738949	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs72738949	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs72738949	GABPB1-AS1	cis	Artery Tibial	GTEx
rs72738949	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs72738949	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs72738949	CTD-3110H11.1	cis	Thyroid	GTEx
rs72738949	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs72738949	GABPB1-AS1	cis	lung	GTEx
rs72738949	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs72738949	GABPB1-AS1	cis	Artery Aorta	GTEx
rs72738949	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs72738949	GABPB1-AS1	cis	Nerve Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50654400-50670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:50656000-50674200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:50658200-50674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:50660800-50669400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:50662400-50672400	Weak transcription	A549	lung
6	chr15:50663200-50670200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:50663400-50669400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:50663400-50674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:50663600-50669600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:50664800-50669400	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links