Variant report

Variant	rs62022567
Chromosome Location	chr15:50597868-50597869
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	chr15:50597253..50599455-chr15:50605376..50607840,2	K562	blood:
2	chr15:50566910..50568792-chr15:50597514..50599198,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1056681	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070770	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070772	1.00[ASN][1000 genomes]
rs11855995	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857071	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903381	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909202	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917303	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509458	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598020	1.00[ASN][1000 genomes]
rs2013885	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013888	0.88[EUR][1000 genomes]
rs2033114	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414049	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450641	1.00[ASN][1000 genomes]
rs45508400	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504781	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022563	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022564	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022565	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022569	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022570	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493426	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677143	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71424053	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72738935	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034849	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920021	1.00[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	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

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs62022567	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs62022567	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs62022567	CTD-3110H11.1	cis	lung	GTEx
rs62022567	GABPB1-AS1	cis	lung	GTEx
rs62022567	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs62022567	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs62022567	GABPB1-AS1	cis	Heart Left Ventricle	GTEx
rs62022567	GABPB1-AS1	cis	Whole Blood	GTEx
rs62022567	CTD-3110H11.1	cis	Stomach	GTEx
rs62022567	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs62022567	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs62022567	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs62022567	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs62022567	GABPB2	Cis_1M	lymphoblastoid	RTeQTL
rs62022567	GABPB1-AS1	cis	Stomach	GTEx
rs62022567	GABPB1-AS1	cis	Artery Tibial	GTEx
rs62022567	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs62022567	GABPB1-AS1	cis	Thyroid	GTEx
rs62022567	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs62022567	CTD-3110H11.1	cis	Thyroid	GTEx
rs62022567	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs62022567	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs62022567	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs62022567	GABPB1-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50568800-50599200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:50570400-50606600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:50570800-50600600	Weak transcription	Spleen	Spleen
4	chr15:50574400-50602000	Weak transcription	Small Intestine	intestine
5	chr15:50575200-50601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:50576600-50599000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:50578200-50600400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:50580400-50599200	Weak transcription	Fetal Brain Male	brain
9	chr15:50580400-50605000	Weak transcription	Fetal Heart	heart
10	chr15:50580800-50600600	Weak transcription	Pancreas	Pancrea
11	chr15:50580800-50638400	Weak transcription	NHEK	skin
12	chr15:50581000-50600600	Weak transcription	Colonic Mucosa	Colon
13	chr15:50585600-50599200	Weak transcription	K562	blood
14	chr15:50586600-50599000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:50586800-50598600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:50586800-50598800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:50586800-50598800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:50587000-50599400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:50587200-50598400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:50587200-50600400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:50588200-50599200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:50589400-50598800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:50589800-50602600	Weak transcription	Gastric	stomach
24	chr15:50592400-50600200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:50592400-50600600	Weak transcription	Esophagus	oesophagus
26	chr15:50592600-50599200	Weak transcription	HSMMtube	muscle
27	chr15:50592600-50600400	Weak transcription	NHLF	lung
28	chr15:50593200-50600000	Weak transcription	Right Ventricle	heart
29	chr15:50593400-50599200	Weak transcription	Brain Germinal Matrix	brain
30	chr15:50593400-50600600	Weak transcription	Psoas Muscle	Psoas
31	chr15:50593400-50602400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:50593600-50598800	Weak transcription	Brain Substantia Nigra	brain
33	chr15:50593600-50599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:50593600-50599400	Weak transcription	Osteobl	bone
35	chr15:50593600-50599800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:50593600-50600000	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:50593600-50600200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:50593600-50600200	Weak transcription	Brain Angular Gyrus	brain
39	chr15:50593600-50600200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:50593600-50600200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:50593600-50600600	Weak transcription	Left Ventricle	heart
42	chr15:50593600-50600600	Weak transcription	Lung	lung
43	chr15:50593600-50602400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:50593600-50605200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:50593800-50599200	Weak transcription	Fetal Kidney	kidney
46	chr15:50593800-50599600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:50593800-50600000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:50593800-50600400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:50594000-50599000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:50594000-50599000	Weak transcription	A549	lung

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