Variant report

Variant	rs9920021
Chromosome Location	chr15:50562149-50562150
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50561224..50565664-chr15:50565813..50569433,4	MCF-7	breast:
2	chr15:50528925..50531452-chr15:50560878..50563779,2	K562	blood:
3	chr15:50532874..50535917-chr15:50560036..50563874,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1056681	1.00[ASN][1000 genomes]
rs11070770	1.00[ASN][1000 genomes]
rs11070772	1.00[ASN][1000 genomes]
rs11855995	1.00[ASN][1000 genomes]
rs11857071	1.00[ASN][1000 genomes]
rs12440601	1.00[ASN][1000 genomes]
rs12903381	1.00[ASN][1000 genomes]
rs12909202	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917303	1.00[ASN][1000 genomes]
rs17509458	1.00[ASN][1000 genomes]
rs2013885	1.00[ASN][1000 genomes]
rs2033114	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2414049	1.00[ASN][1000 genomes]
rs28450641	1.00[ASN][1000 genomes]
rs45508400	1.00[ASN][1000 genomes]
rs504781	1.00[ASN][1000 genomes]
rs62022563	1.00[ASN][1000 genomes]
rs62022564	1.00[ASN][1000 genomes]
rs62022565	1.00[ASN][1000 genomes]
rs62022567	1.00[ASN][1000 genomes]
rs62022569	1.00[ASN][1000 genomes]
rs62022570	1.00[ASN][1000 genomes]
rs6493426	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677143	1.00[ASN][1000 genomes]
rs72738935	1.00[ASN][1000 genomes]
rs8034849	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs9920021	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs9920021	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs9920021	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs9920021	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs9920021	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs9920021	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs9920021	GABPB1-AS1	cis	Artery Tibial	GTEx
rs9920021	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs9920021	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs9920021	GABPB1-AS1	cis	lung	GTEx
rs9920021	GABPB1-AS1	cis	Thyroid	GTEx
rs9920021	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs9920021	GABPB1-AS1	cis	Artery Aorta	GTEx
rs9920021	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9920021	GABPB1-AS1	cis	Whole Blood	GTEx
rs9920021	GABPB1-AS1	cis	Stomach	GTEx
rs9920021	CTD-3110H11.1	cis	Stomach	GTEx
rs9920021	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs9920021	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs9920021	CTD-3110H11.1	cis	lung	GTEx
rs9920021	GABPB2	Cis_1M	lymphoblastoid	RTeQTL
rs9920021	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs9920021	CTD-3110H11.1	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50555400-50579400	Weak transcription	K562	blood
2	chr15:50558000-50572400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:50558200-50563800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50558600-50569800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links