Variant report

Variant	rs62259939
Chromosome Location	chr3:49386047-49386048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49385664..49387593-chr3:49457975..49460333,2	K562	blood:
2	chr3:49385803..49389031-chr3:49447399..49451143,5	K562	blood:
3	chr3:49376089..49379418-chr3:49384584..49389123,6	K562	blood:
4	chr3:49385523..49388550-chr3:49394955..49397439,3	K562	blood:
5	chr3:49376745..49379298-chr3:49384391..49386630,2	K562	blood:

Variant related genes	Relation type
ENSG00000145020	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000233276	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000067560	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1050450	0.94[ASN][1000 genomes]
rs10865955	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130192	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130194	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130196	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130199	0.83[EUR][1000 genomes]
rs11711536	0.94[ASN][1000 genomes]
rs11716974	0.82[ASN][1000 genomes]
rs13086611	0.94[ASN][1000 genomes]
rs13087851	0.94[ASN][1000 genomes]
rs13090388	0.94[ASN][1000 genomes]
rs13096760	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1464566	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	0.83[EUR][1000 genomes]
rs1568662	0.82[EUR][1000 genomes]
rs17080528	0.94[ASN][1000 genomes]
rs17595772	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650792	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800668	0.94[ASN][1000 genomes]
rs1987628	0.94[ASN][1000 genomes]
rs2117939	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2878298	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34588335	0.94[ASN][1000 genomes]
rs34937635	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35169793	0.94[ASN][1000 genomes]
rs35701831	0.83[EUR][1000 genomes]
rs3811699	0.94[ASN][1000 genomes]
rs3877784	0.83[EUR][1000 genomes]
rs3924462	0.83[EUR][1000 genomes]
rs4459909	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4563439	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4855842	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4855843	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855859	0.84[EUR][1000 genomes]
rs4855861	0.81[EUR][1000 genomes]
rs4855864	0.83[EUR][1000 genomes]
rs4855866	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855873	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955412	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955438	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55957735	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59152804	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62259942	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62261185	0.80[EUR][1000 genomes]
rs6446264	0.94[ASN][1000 genomes]
rs6446274	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67485053	0.88[ASN][1000 genomes]
rs6773518	0.93[EUR][1000 genomes]
rs6784820	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792911	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793308	0.94[ASN][1000 genomes]
rs6797765	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809216	0.94[ASN][1000 genomes]
rs7371895	0.81[EUR][1000 genomes]
rs7373849	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621003	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623659	0.94[ASN][1000 genomes]
rs7631908	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637999	0.83[EUR][1000 genomes]
rs7643586	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643845	0.83[EUR][1000 genomes]
rs7645445	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7648841	0.94[ASN][1000 genomes]
rs885592	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62259939	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs62259939	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs62259939	WDR6	cis	lung	GTEx
rs62259939	AMT	cis	Thyroid	GTEx
rs62259939	WDR6	cis	Adipose Subcutaneous	GTEx
rs62259939	WDR6	cis	Artery Tibial	GTEx
rs62259939	WDR6	cis	Whole Blood	GTEx
rs62259939	WDR6	cis	Muscle Skeletal	GTEx
rs62259939	WDR6	cis	Nerve Tibial	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49378600-49386400	Weak transcription	K562	blood
2	chr3:49378600-49386600	Weak transcription	Stomach Mucosa	stomach
3	chr3:49378600-49386800	Weak transcription	Gastric	stomach
4	chr3:49378600-49388400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:49378600-49388800	Weak transcription	Brain Substantia Nigra	brain
6	chr3:49378600-49388800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:49378600-49390000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:49378600-49392000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:49378800-49386800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:49378800-49387400	Weak transcription	Esophagus	oesophagus
11	chr3:49379000-49392000	Weak transcription	Left Ventricle	heart
12	chr3:49379800-49386600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:49379800-49392800	Weak transcription	Thymus	Thymus
14	chr3:49381400-49388800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:49381600-49393000	Weak transcription	Right Atrium	heart
16	chr3:49382200-49386400	Weak transcription	Liver	Liver
17	chr3:49382200-49388200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:49383000-49386400	Enhancers	Primary B cells from cord blood	blood
19	chr3:49383000-49386800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:49383000-49388800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:49383000-49388800	Weak transcription	Fetal Thymus	thymus
22	chr3:49383000-49389200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:49383000-49389400	Weak transcription	Spleen	Spleen
24	chr3:49383000-49393600	Weak transcription	Primary T cells from cord blood	blood
25	chr3:49383200-49391800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:49383200-49392400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:49383400-49388200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:49383400-49388200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:49383400-49389000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr3:49383400-49391400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:49383600-49388600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:49384000-49388400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:49384400-49386400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:49384400-49388200	Weak transcription	NHLF	lung
35	chr3:49384600-49386800	Weak transcription	HUVEC	blood vessel
36	chr3:49384600-49387400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:49384600-49388200	Weak transcription	HSMM	muscle
38	chr3:49384600-49388800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:49384600-49388800	Weak transcription	HSMMtube	muscle
40	chr3:49384600-49389000	Weak transcription	NH-A	brain
41	chr3:49384600-49392000	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:49384600-49392400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:49384800-49386200	Weak transcription	HepG2	liver
44	chr3:49384800-49386400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:49384800-49386400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:49384800-49386600	Weak transcription	Lung	lung
47	chr3:49384800-49386800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:49384800-49386800	Weak transcription	GM12878-XiMat	blood
49	chr3:49384800-49387000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:49384800-49387200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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