Variant report

Variant	rs28567949
Chromosome Location	chr3:48744560-48744561
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	chr3:48727679..48729192-chr3:48743162..48745800,2	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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	0.97[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	0.95[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	0.97[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]
rs13090013	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13324950	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	0.97[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	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28657585	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096717	0.82[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	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	0.97[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	0.95[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	0.95[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	0.97[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	0.84[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	0.97[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
rs28567949	WDR6	cis	Adipose Subcutaneous	GTEx
rs28567949	WDR6	cis	Whole Blood	GTEx
rs28567949	WDR6	cis	lung	GTEx
rs28567949	WDR6	cis	Esophagus Mucosa	GTEx
rs28567949	WDR6	cis	Skin Sun Exposed Lower leg	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	chr3:48733200-48746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:48733200-48746000	Strong transcription	Fetal Intestine Small	intestine
11	chr3:48733200-48746200	Weak transcription	Right Ventricle	heart
12	chr3:48734000-48746400	Weak transcription	Fetal Brain Male	brain
13	chr3:48734200-48745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:48734400-48744600	Weak transcription	NHLF	lung
15	chr3:48734400-48745600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:48734400-48746000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:48734400-48746000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:48734400-48746200	Weak transcription	Gastric	stomach
19	chr3:48734400-48746400	Weak transcription	Stomach Mucosa	stomach
20	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:48735800-48746000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:48737200-48744800	Weak transcription	Fetal Kidney	kidney
23	chr3:48737200-48746200	Weak transcription	Pancreas	Pancrea
24	chr3:48737200-48746200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:48737200-48746600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:48737400-48746400	Weak transcription	HSMMtube	muscle
27	chr3:48738000-48746000	Weak transcription	K562	blood
28	chr3:48738200-48752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:48738400-48745200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:48738400-48746200	Weak transcription	Brain Angular Gyrus	brain
31	chr3:48738800-48744800	Weak transcription	Left Ventricle	heart
32	chr3:48738800-48746200	Weak transcription	Fetal Brain Female	brain
33	chr3:48739000-48744600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:48739400-48745800	Strong transcription	Osteobl	bone
35	chr3:48739800-48750800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:48740000-48744800	Weak transcription	Brain Germinal Matrix	brain
37	chr3:48740000-48745800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:48740000-48746200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:48740200-48744600	Strong transcription	HMEC	breast
41	chr3:48740400-48744600	Weak transcription	Right Atrium	heart
42	chr3:48740400-48745000	Weak transcription	Ovary	ovary
43	chr3:48740400-48746600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:48740600-48744600	Weak transcription	Liver	Liver
45	chr3:48740600-48745200	Weak transcription	NHDF-Ad	bronchial
46	chr3:48740600-48745400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:48740600-48747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:48740800-48746000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:48740800-48746000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:48740800-48746000	Weak transcription	Fetal Heart	heart

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