Variant report

Variant	rs13090013
Chromosome Location	chr3:48742578-48742579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48736950..48739890-chr3:48741169..48743085,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10865952	0.95[ASN][1000 genomes]
rs11557629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708786	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715177	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.81[ASN][1000 genomes]
rs11719291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719457	0.80[AMR][1000 genomes]
rs12107418	0.81[EUR][1000 genomes]
rs12493578	0.95[ASN][1000 genomes]
rs12497850	0.95[ASN][1000 genomes]
rs12715429	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13063223	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070798	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13076269	0.81[AMR][1000 genomes]
rs13086240	0.84[AMR][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13324950	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	0.95[ASN][1000 genomes]
rs17080319	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2286652	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28452701	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28567949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096717	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34153629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577723	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3821875	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4077495	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	0.95[ASN][1000 genomes]
rs4858828	0.95[ASN][1000 genomes]
rs4858831	0.95[ASN][1000 genomes]
rs56735597	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61137521	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768448	0.85[EUR][1000 genomes]
rs6773261	0.81[AMR][1000 genomes]
rs6788650	0.95[ASN][1000 genomes]
rs68042649	0.85[EUR][1000 genomes]
rs73078362	0.81[EUR][1000 genomes]
rs7633840	0.86[ASN][1000 genomes]
rs9809222	0.85[EUR][1000 genomes]
rs9811027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	0.85[EUR][1000 genomes]
rs9812200	0.83[EUR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9821797	0.85[EUR][1000 genomes]
rs9834996	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836462	0.85[EUR][1000 genomes]
rs9841602	0.85[EUR][1000 genomes]
rs9848203	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873726	0.85[EUR][1000 genomes]
rs9877542	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882549	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13090013	WDR6	cis	Esophagus Mucosa	GTEx
rs13090013	WDR6	cis	Adipose Subcutaneous	GTEx
rs13090013	WDR6	cis	Whole Blood	GTEx
rs13090013	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13090013	WDR6	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
2	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
5	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
6	chr3:48733000-48744800	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:48733000-48745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
9	chr3:48733200-48744000	Weak transcription	Esophagus	oesophagus
10	chr3:48733200-48746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:48733200-48746000	Strong transcription	Fetal Intestine Small	intestine
12	chr3:48733200-48746200	Weak transcription	Right Ventricle	heart
13	chr3:48734000-48746400	Weak transcription	Fetal Brain Male	brain
14	chr3:48734200-48745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:48734400-48744600	Weak transcription	NHLF	lung
16	chr3:48734400-48745600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:48734400-48746000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:48734400-48746000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:48734400-48746200	Weak transcription	Gastric	stomach
20	chr3:48734400-48746400	Weak transcription	Stomach Mucosa	stomach
21	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:48735800-48743000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:48735800-48744000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:48735800-48746000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:48737200-48742800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:48737200-48744000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:48737200-48744800	Weak transcription	Fetal Kidney	kidney
28	chr3:48737200-48746200	Weak transcription	Pancreas	Pancrea
29	chr3:48737200-48746200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:48737200-48746600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:48737400-48743600	Weak transcription	Spleen	Spleen
32	chr3:48737400-48746400	Weak transcription	HSMMtube	muscle
33	chr3:48738000-48743600	Weak transcription	Colonic Mucosa	Colon
34	chr3:48738000-48744200	Weak transcription	HepG2	liver
35	chr3:48738000-48746000	Weak transcription	K562	blood
36	chr3:48738200-48752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:48738400-48743000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:48738400-48743600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:48738400-48745200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:48738400-48746200	Weak transcription	Brain Angular Gyrus	brain
41	chr3:48738600-48742600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:48738600-48743000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:48738600-48743800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:48738800-48742800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:48738800-48742800	Weak transcription	Placenta	Placenta
46	chr3:48738800-48744800	Weak transcription	Left Ventricle	heart
47	chr3:48738800-48746200	Weak transcription	Fetal Brain Female	brain
48	chr3:48739000-48744600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:48739400-48745800	Strong transcription	Osteobl	bone
50	chr3:48739600-48744200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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