Variant report

Variant	rs62259942
Chromosome Location	chr3:49422687-49422688
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1050450	0.83[ASN][1000 genomes]
rs10865955	0.81[AMR][1000 genomes]
rs11130192	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11130193	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11130194	0.81[EUR][1000 genomes]
rs11130196	0.85[AMR][1000 genomes]
rs11711536	0.83[ASN][1000 genomes]
rs13086611	0.83[ASN][1000 genomes]
rs13087851	0.83[ASN][1000 genomes]
rs13090388	0.83[ASN][1000 genomes]
rs13096760	0.82[EUR][1000 genomes]
rs1464566	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1464567	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1464568	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17080528	0.83[ASN][1000 genomes]
rs17595772	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17650792	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800668	0.83[ASN][1000 genomes]
rs1987628	0.83[ASN][1000 genomes]
rs2117939	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2878298	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34588335	0.83[ASN][1000 genomes]
rs34937635	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35169793	0.83[ASN][1000 genomes]
rs3811699	0.83[ASN][1000 genomes]
rs4459909	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4563439	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4855842	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4855843	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855866	0.82[AMR][1000 genomes]
rs4855873	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855877	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4955412	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4955438	0.90[AMR][1000 genomes]
rs55957735	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59152804	0.87[AMR][1000 genomes]
rs62259939	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446264	0.83[ASN][1000 genomes]
rs6446274	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6773518	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6784820	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6792911	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6793308	0.83[ASN][1000 genomes]
rs6797765	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6809216	0.83[ASN][1000 genomes]
rs7373849	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7621003	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623659	0.83[ASN][1000 genomes]
rs7631908	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7643586	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7645445	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7648841	0.83[ASN][1000 genomes]
rs885592	0.82[AMR][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62259942	WDR6	cis	Muscle Skeletal	GTEx
rs62259942	WDR6	cis	Nerve Tibial	GTEx
rs62259942	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs62259942	WDR6	cis	Adipose Subcutaneous	GTEx
rs62259942	WDR6	cis	lung	GTEx
rs62259942	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs62259942	WDR6	cis	Whole Blood	GTEx
rs62259942	WDR6	cis	Artery Tibial	GTEx
rs62259942	AMT	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49397200-49423800	Weak transcription	Fetal Heart	heart
3	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:49411000-49434600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:49411200-49423200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:49411200-49423800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:49413000-49423200	Weak transcription	Brain Anterior Caudate	brain
9	chr3:49413000-49423800	Weak transcription	HUVEC	blood vessel
10	chr3:49413200-49423200	Weak transcription	Primary T cells from cord blood	blood
11	chr3:49413200-49423200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:49413200-49423200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:49413200-49425400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:49413200-49425600	Weak transcription	Hela-S3	cervix
15	chr3:49413200-49431800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:49413200-49432000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:49413200-49432000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:49413200-49432000	Weak transcription	Fetal Kidney	kidney
19	chr3:49413200-49433200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:49413200-49435000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:49413200-49441400	Weak transcription	Aorta	Aorta
22	chr3:49413200-49443000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:49413400-49423200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:49413400-49425400	Weak transcription	Thymus	Thymus
26	chr3:49413400-49425400	Weak transcription	Dnd41	blood
27	chr3:49413400-49425600	Weak transcription	Fetal Intestine Large	intestine
28	chr3:49413400-49431800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:49413400-49433600	Weak transcription	Brain Germinal Matrix	brain
30	chr3:49413400-49439000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:49413600-49430600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:49413600-49432000	Weak transcription	Fetal Lung	lung
33	chr3:49413600-49433200	Weak transcription	Colonic Mucosa	Colon
34	chr3:49413600-49441000	Weak transcription	Fetal Brain Female	brain
35	chr3:49413800-49425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:49414400-49423200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:49414600-49424400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:49414600-49424400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr3:49414800-49424200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:49415400-49423200	Weak transcription	A549	lung
41	chr3:49415800-49425400	Weak transcription	Fetal Thymus	thymus
42	chr3:49416200-49423600	Weak transcription	Liver	Liver
43	chr3:49416200-49425400	Weak transcription	Spleen	Spleen
44	chr3:49416200-49430400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:49416200-49431800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:49416200-49433200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:49416200-49435200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:49416400-49425400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:49416400-49425400	Weak transcription	Fetal Intestine Small	intestine
50	chr3:49416400-49425400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links