Variant report

Variant	rs1365504
Chromosome Location	chr15:50591180-50591181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50591033..50592808-chr15:50595197..50598037,2	K562	blood:

Variant related genes	Relation type
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs10152534	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10220734	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10220755	0.95[ASN][1000 genomes]
rs11070766	0.80[EUR][1000 genomes]
rs11631985	0.80[EUR][1000 genomes]
rs11632703	0.81[EUR][1000 genomes]
rs11633903	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11636564	0.80[EUR][1000 genomes]
rs11638319	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638432	0.80[EUR][1000 genomes]
rs11638564	0.81[EUR][1000 genomes]
rs12594956	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12901373	0.95[ASN][1000 genomes]
rs12913144	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16963604	0.80[EUR][1000 genomes]
rs1797311	0.81[EUR][1000 genomes]
rs1972699	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081628	0.80[EUR][1000 genomes]
rs2114447	0.96[ASN][1000 genomes]
rs28716586	0.80[EUR][1000 genomes]
rs28886692	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34590486	0.80[EUR][1000 genomes]
rs35000991	0.81[EUR][1000 genomes]
rs35777196	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3784297	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3985829	0.95[ASN][1000 genomes]
rs4775874	0.80[EUR][1000 genomes]
rs4775875	0.80[EUR][1000 genomes]
rs489345	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs535648	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62022573	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493425	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493427	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493430	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168233	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8026785	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030036	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8031431	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8039829	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8041259	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8042451	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8042845	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043257	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1365504	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1365504	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs1365504	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs1365504	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs1365504	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs1365504	CTD-3110H11.1	cis	lung	GTEx
rs1365504	CTD-3110H11.1	cis	Thyroid	GTEx
rs1365504	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs1365504	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs1365504	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs1365504	GABPB1-AS1	cis	Artery Aorta	GTEx
rs1365504	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs1365504	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1365504	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs1365504	GABPB1-AS1	cis	Artery Tibial	GTEx
rs1365504	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs1365504	GABPB1-AS1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50567600-50593000	Weak transcription	NHDF-Ad	bronchial
2	chr15:50568000-50593400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:50568200-50592000	Weak transcription	NHLF	lung
4	chr15:50568800-50591800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:50568800-50592200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:50568800-50599200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:50569200-50591800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:50569200-50592200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:50570000-50591800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:50570200-50591800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:50570400-50606600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:50570800-50591800	Weak transcription	HSMMtube	muscle
13	chr15:50570800-50600600	Weak transcription	Spleen	Spleen
14	chr15:50571000-50592000	Weak transcription	Right Ventricle	heart
15	chr15:50571200-50593000	Weak transcription	Fetal Kidney	kidney
16	chr15:50572800-50593200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:50573000-50592000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:50574400-50602000	Weak transcription	Small Intestine	intestine
19	chr15:50574800-50592000	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:50575200-50601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:50576000-50592000	Weak transcription	Brain Anterior Caudate	brain
22	chr15:50576600-50599000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:50578200-50592000	Weak transcription	NH-A	brain
24	chr15:50578200-50600400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:50578400-50597800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:50578600-50591200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:50578600-50592000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:50578600-50592600	Weak transcription	Brain Angular Gyrus	brain
29	chr15:50579200-50592000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:50579200-50593400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:50580400-50591400	Weak transcription	Osteobl	bone
32	chr15:50580400-50599200	Weak transcription	Fetal Brain Male	brain
33	chr15:50580400-50605000	Weak transcription	Fetal Heart	heart
34	chr15:50580600-50596000	Weak transcription	Fetal Brain Female	brain
35	chr15:50580800-50591800	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:50580800-50591800	Weak transcription	Esophagus	oesophagus
37	chr15:50580800-50591800	Weak transcription	A549	lung
38	chr15:50580800-50592000	Weak transcription	Brain Germinal Matrix	brain
39	chr15:50580800-50600600	Weak transcription	Pancreas	Pancrea
40	chr15:50580800-50638400	Weak transcription	NHEK	skin
41	chr15:50581000-50600600	Weak transcription	Colonic Mucosa	Colon
42	chr15:50581200-50591800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:50581200-50592000	Weak transcription	HepG2	liver
44	chr15:50581200-50594600	Weak transcription	Aorta	Aorta
45	chr15:50581800-50591600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:50581800-50592800	Weak transcription	Brain Substantia Nigra	brain
47	chr15:50582200-50591800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:50582200-50597800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:50582400-50591800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:50585600-50599200	Weak transcription	K562	blood

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