Variant report

Variant	rs6563116
Chromosome Location	chr13:80096111-80096112
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:80088753..80091957-chr13:80093652..80097974,3	K562	blood:
2	chr13:80094980..80096725-chr13:80098765..80101682,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1208049	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1212082	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1335368	0.92[ASN][1000 genomes]
rs1335370	0.91[ASN][1000 genomes]
rs1408049	0.92[ASN][1000 genomes]
rs1414155	0.91[ASN][1000 genomes]
rs1414156	0.91[ASN][1000 genomes]
rs1475797	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1577416	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1577418	0.91[ASN][1000 genomes]
rs2065743	0.92[ASN][1000 genomes]
rs2181433	0.82[ASN][1000 genomes]
rs2476172	0.83[ASN][1000 genomes]
rs2476173	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484343	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2484344	0.83[ASN][1000 genomes]
rs2484345	0.81[AMR][1000 genomes]
rs2760101	0.90[ASN][1000 genomes]
rs2760102	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2760103	0.91[ASN][1000 genomes]
rs2760105	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2760106	0.94[ASN][1000 genomes]
rs2783119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783120	0.94[ASN][1000 genomes]
rs2783121	0.93[ASN][1000 genomes]
rs2783122	0.93[ASN][1000 genomes]
rs2783125	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2783126	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs314688	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs386603	0.81[ASN][1000 genomes]
rs4145207	0.91[ASN][1000 genomes]
rs4476060	0.82[ASN][1000 genomes]
rs4885633	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4885634	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4885636	0.92[ASN][1000 genomes]
rs6563110	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6563113	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6563115	0.94[ASN][1000 genomes]
rs700396	0.90[ASN][1000 genomes]
rs7321953	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73235963	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7325095	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7338530	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7339303	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7982263	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7988601	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7990344	0.91[ASN][1000 genomes]
rs7996493	0.89[ASN][1000 genomes]
rs8002042	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9318644	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9530922	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9530925	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9545142	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9565510	0.94[ASN][1000 genomes]
rs9574429	0.82[ASN][1000 genomes]
rs9574434	0.95[ASN][1000 genomes]
rs9593399	0.82[ASN][1000 genomes]
rs9601240	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9601242	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs987284	0.91[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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv916983	chr13:80065879-80249702	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6563116	RP11-25J23.3	cis	lung	GTEx
rs6563116	RP11-25J23.3	cis	Thyroid	GTEx
rs6563116	RBM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80066800-80122800	Weak transcription	Esophagus	oesophagus
2	chr13:80070600-80096600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:80076000-80099200	Weak transcription	Hela-S3	cervix
4	chr13:80078000-80097200	Weak transcription	Psoas Muscle	Psoas
5	chr13:80078000-80097800	Weak transcription	Ovary	ovary
6	chr13:80078200-80102000	Weak transcription	Right Ventricle	heart
7	chr13:80079600-80098200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:80082800-80096600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:80082800-80096600	Weak transcription	Lung	lung
10	chr13:80082800-80108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr13:80083000-80120000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:80083000-80122800	Weak transcription	Stomach Mucosa	stomach
13	chr13:80083400-80096200	Weak transcription	Left Ventricle	heart
14	chr13:80085000-80096800	Weak transcription	Primary T cells from cord blood	blood
15	chr13:80086800-80098400	Weak transcription	Brain Substantia Nigra	brain
16	chr13:80087400-80134000	Weak transcription	Aorta	Aorta
17	chr13:80087400-80134600	Weak transcription	Pancreas	Pancrea
18	chr13:80087800-80096600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr13:80089000-80096600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:80089200-80098800	Weak transcription	Brain Angular Gyrus	brain
21	chr13:80089400-80097800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:80089400-80098800	Weak transcription	Brain Anterior Caudate	brain
23	chr13:80089400-80098800	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:80089400-80099200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr13:80089400-80118400	Weak transcription	Small Intestine	intestine
26	chr13:80090400-80096600	Weak transcription	HUVEC	blood vessel
27	chr13:80090600-80112000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr13:80090800-80103400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr13:80091000-80099200	Weak transcription	K562	blood
30	chr13:80091400-80096600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:80091400-80108000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:80091600-80097800	Weak transcription	Fetal Heart	heart
33	chr13:80091600-80097800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr13:80092200-80109400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr13:80092400-80096200	Weak transcription	Fetal Kidney	kidney
36	chr13:80092400-80096200	Weak transcription	GM12878-XiMat	blood
37	chr13:80092400-80099200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr13:80092400-80102000	Weak transcription	Colonic Mucosa	Colon
39	chr13:80093000-80110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:80093200-80096800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr13:80093400-80097800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr13:80093400-80097800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:80093400-80098400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr13:80093400-80104200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr13:80093400-80112800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:80093600-80096600	Weak transcription	HepG2	liver
47	chr13:80093600-80096600	Weak transcription	HSMMtube	muscle
48	chr13:80093600-80098400	Weak transcription	Fetal Muscle Leg	muscle
49	chr13:80093600-80108200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr13:80093800-80096400	Genic enhancers	Dnd41	blood

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