Variant report

Variant	rs4241408
Chromosome Location	chr3:49517216-49517217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1050088	0.90[EUR][1000 genomes]
rs10865955	0.92[EUR][1000 genomes]
rs11130192	0.83[EUR][1000 genomes]
rs11130193	0.86[EUR][1000 genomes]
rs11130194	0.84[EUR][1000 genomes]
rs11130196	0.89[EUR][1000 genomes]
rs11130199	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11130202	0.92[EUR][1000 genomes]
rs11130206	0.88[EUR][1000 genomes]
rs11720264	0.91[EUR][1000 genomes]
rs12488065	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12489092	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13096760	0.87[EUR][1000 genomes]
rs1464566	0.82[EUR][1000 genomes]
rs1464567	0.83[EUR][1000 genomes]
rs1464568	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1568661	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1568662	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2312461	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34937635	0.81[EUR][1000 genomes]
rs35701831	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3870337	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3870338	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3877784	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3924462	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3924463	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4241406	0.90[EUR][1000 genomes]
rs4459909	0.83[EUR][1000 genomes]
rs4855836	0.90[EUR][1000 genomes]
rs4855839	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855842	0.82[EUR][1000 genomes]
rs4855843	0.81[EUR][1000 genomes]
rs4855855	0.90[EUR][1000 genomes]
rs4855859	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855861	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4855864	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4855866	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4855873	0.82[EUR][1000 genomes]
rs4855877	0.82[EUR][1000 genomes]
rs55957735	0.82[EUR][1000 genomes]
rs59152804	0.88[EUR][1000 genomes]
rs62261185	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6773518	0.81[EUR][1000 genomes]
rs6784820	0.83[EUR][1000 genomes]
rs6792911	0.81[EUR][1000 genomes]
rs6797765	0.81[EUR][1000 genomes]
rs7371895	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7631908	0.81[EUR][1000 genomes]
rs7637665	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7637999	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7643586	0.82[EUR][1000 genomes]
rs7643845	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7645445	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs885592	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4241408	WDR6	cis	Muscle Skeletal	GTEx
rs4241408	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4241408	WDR6	cis	lung	GTEx
rs4241408	WDR6	cis	Adipose Subcutaneous	GTEx
rs4241408	AMT	cis	Thyroid	GTEx
rs4241408	WDR6	cis	Whole Blood	GTEx
rs4241408	WDR6	cis	Nerve Tibial	GTEx
rs4241408	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509400-49520200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:49509600-49519000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:49509600-49522800	Weak transcription	Brain Angular Gyrus	brain
4	chr3:49509600-49530800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:49509800-49520800	Weak transcription	Ovary	ovary
7	chr3:49509800-49522800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:49509800-49522800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:49509800-49522800	Weak transcription	NHEK	skin
10	chr3:49509800-49523000	Weak transcription	Brain Substantia Nigra	brain
11	chr3:49509800-49531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:49510000-49520000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:49510000-49520200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:49510000-49520800	Weak transcription	Right Atrium	heart
17	chr3:49510000-49521200	Weak transcription	HepG2	liver
18	chr3:49510000-49521400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:49510000-49522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:49510000-49523200	Weak transcription	Fetal Kidney	kidney
21	chr3:49510000-49526800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:49510000-49535600	Weak transcription	NHLF	lung
23	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:49510800-49518000	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:49511000-49518800	Weak transcription	K562	blood
26	chr3:49511400-49518600	Strong transcription	Fetal Intestine Small	intestine
27	chr3:49511400-49522800	Weak transcription	Stomach Mucosa	stomach
28	chr3:49511800-49518200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:49513400-49517400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:49514000-49519400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:49514200-49517400	Strong transcription	Thymus	Thymus
32	chr3:49514200-49522000	Weak transcription	NHDF-Ad	bronchial
33	chr3:49514400-49518000	Strong transcription	Fetal Stomach	stomach
34	chr3:49514400-49518800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:49514400-49518800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:49514400-49519200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:49514400-49520000	Strong transcription	Fetal Thymus	thymus
38	chr3:49514400-49521200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:49514400-49522000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:49514400-49522800	Weak transcription	Osteobl	bone
41	chr3:49514400-49532400	Weak transcription	GM12878-XiMat	blood
42	chr3:49514600-49521800	Weak transcription	HSMM	muscle
43	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:49514800-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:49515000-49519000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:49515000-49521800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:49515000-49532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:49515000-49535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:49515200-49520800	Weak transcription	Psoas Muscle	Psoas
50	chr3:49515200-49521200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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