Variant report

Variant	rs17509458
Chromosome Location	chr15:50665362-50665363
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50661266..50664034-chr15:50664188..50666588,3	MCF-7	breast:
2	chr15:50661068..50663929-chr15:50664392..50666843,2	K562	blood:
3	chr15:50665109..50666861-chr15:50668510..50670054,2	K562	blood:
4	chr15:50642965..50650579-chr15:50662841..50666750,8	K562	blood:
5	chr15:50664439..50666411-chr15:50707371..50708947,2	MCF-7	breast:
6	chr15:50664721..50667463-chr15:50714683..50717167,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138592	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 24 )

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

rs_ID	r²[population]
rs1056681	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070770	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070772	1.00[ASN][1000 genomes]
rs11855995	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857071	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440601	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903381	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909202	1.00[ASN][1000 genomes]
rs12917303	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598020	1.00[ASN][1000 genomes]
rs2013885	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013888	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2033114	1.00[ASN][1000 genomes]
rs2414049	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450641	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45508400	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504781	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022563	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022564	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022565	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022567	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022569	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022570	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493426	1.00[ASN][1000 genomes]
rs6493439	0.81[EUR][1000 genomes]
rs677143	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71424053	0.81[EUR][1000 genomes]
rs72738935	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72738949	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8034849	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920021	1.00[ASN][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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs17509458	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs17509458	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs17509458	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs17509458	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs17509458	CTD-3110H11.1	cis	Stomach	GTEx
rs17509458	GABPB2	Cis_1M	lymphoblastoid	RTeQTL
rs17509458	GABPB1-AS1	cis	Thyroid	GTEx
rs17509458	GABPB1-AS1	cis	lung	GTEx
rs17509458	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs17509458	CTD-3110H11.1	cis	lung	GTEx
rs17509458	GABPB1-AS1	cis	Stomach	GTEx
rs17509458	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs17509458	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs17509458	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs17509458	GABPB1-AS1	cis	Artery Tibial	GTEx
rs17509458	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs17509458	CTD-3110H11.1	cis	Thyroid	GTEx
rs17509458	GABPB1-AS1	cis	Whole Blood	GTEx
rs17509458	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs17509458	GABPB1-AS1	cis	Heart Left Ventricle	GTEx
rs17509458	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs17509458	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs17509458	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs17509458	GABPB1-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50653200-50666800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:50654400-50666400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:50654400-50670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:50654600-50666000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:50655600-50665400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:50655800-50666000	Weak transcription	Brain Germinal Matrix	brain
8	chr15:50655800-50666000	Weak transcription	Left Ventricle	heart
9	chr15:50656000-50665800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:50656000-50674200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:50657200-50668200	Weak transcription	HSMM	muscle
12	chr15:50657400-50666000	Weak transcription	HSMMtube	muscle
13	chr15:50658200-50674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:50660800-50669400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:50662400-50672400	Weak transcription	A549	lung
16	chr15:50663200-50665600	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:50663200-50670200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:50663400-50669400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:50663400-50674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:50663600-50669600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:50664800-50669400	Weak transcription	Primary T cells from cord blood	blood

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