Variant report

Variant	rs12594062
Chromosome Location	chr15:75102851-75102852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75088510..75091913-chr15:75102419..75105144,4	K562	blood:
2	chr15:75101293..75104748-chr15:75109733..75112723,4	K562	blood:
3	chr15:75059199..75061491-chr15:75101386..75103400,2	MCF-7	breast:
4	chr15:75101475..75103116-chr15:75104529..75106195,2	K562	blood:

Variant related genes	Relation type
ENSG00000140506	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11072507	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11072508	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632414	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11635664	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636952	0.81[EUR][1000 genomes]
rs12591513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898997	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903541	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12903896	0.82[AMR][1000 genomes]
rs12905199	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12917376	0.95[ASN][1000 genomes]
rs1378940	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378941	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378942	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2168518	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470890	0.84[AMR][1000 genomes]
rs2472304	0.84[AMR][1000 genomes]
rs2960192	0.84[AMR][1000 genomes]
rs34862454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784789	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886410	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62006567	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12594062	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12594062	SCAMP5	cis	lung	GTEx
rs12594062	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75086000-75107400	Weak transcription	Fetal Brain Male	brain
2	chr15:75096000-75109000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:75096200-75105200	Weak transcription	Fetal Lung	lung
4	chr15:75096200-75109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:75096400-75104800	Weak transcription	Right Ventricle	heart
6	chr15:75096600-75107200	Weak transcription	Gastric	stomach
7	chr15:75096600-75107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:75096800-75104800	Weak transcription	Ovary	ovary
9	chr15:75096800-75107200	Weak transcription	Pancreas	Pancrea
10	chr15:75096800-75107200	Weak transcription	A549	lung
11	chr15:75096800-75107400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:75096800-75107400	Weak transcription	HSMMtube	muscle
13	chr15:75096800-75109000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:75096800-75109200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:75096800-75109400	Weak transcription	HUVEC	blood vessel
16	chr15:75096800-75109800	Weak transcription	NH-A	brain
17	chr15:75097000-75107200	Weak transcription	Spleen	Spleen
18	chr15:75097000-75107600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:75097000-75109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:75097000-75109400	Weak transcription	Brain Anterior Caudate	brain
21	chr15:75097200-75108000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr15:75097200-75109400	Weak transcription	Lung	lung
23	chr15:75097600-75103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:75097600-75108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:75097600-75111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:75097800-75107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:75097800-75109200	Weak transcription	Brain Germinal Matrix	brain
28	chr15:75100400-75103200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:75100800-75104800	Weak transcription	Left Ventricle	heart
30	chr15:75100800-75105200	Weak transcription	Right Atrium	heart
31	chr15:75100800-75107800	Weak transcription	GM12878-XiMat	blood
32	chr15:75101000-75105000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:75101200-75107200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:75101200-75109000	Weak transcription	HMEC	breast
35	chr15:75101800-75103000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:75101800-75104800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:75101800-75107200	Weak transcription	Colonic Mucosa	Colon
38	chr15:75101800-75107200	Weak transcription	Esophagus	oesophagus
39	chr15:75101800-75109200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr15:75101800-75113200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:75102000-75104600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:75102000-75107400	Weak transcription	Placenta	Placenta
43	chr15:75102000-75108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:75102400-75107600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:75102600-75105600	Weak transcription	Hela-S3	cervix
46	chr15:75102600-75109600	Weak transcription	NHLF	lung
47	chr15:75102800-75103000	Enhancers	Muscle Satellite Cultured Cells	--

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