Variant report

Variant	rs13080725
Chromosome Location	chr3:49076092-49076093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49076051-49076538	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:49075986-49076104	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49070617..49072878-chr3:49076059..49078108,2	K562	blood:
2	chr3:49073963..49076369-chr3:49168247..49170287,2	K562	blood:

Variant related genes	Relation type
QRICH1	TF binding region
ENSG00000198218	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10154895	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11552724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706189	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11708022	0.85[AMR][1000 genomes]
rs11709092	0.81[AMR][1000 genomes]
rs11709246	0.85[AMR][1000 genomes]
rs11710247	0.81[EUR][1000 genomes]
rs11712006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713297	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11713694	0.85[AMR][1000 genomes]
rs11715689	0.89[AMR][1000 genomes]
rs11715713	0.89[AMR][1000 genomes]
rs11715835	0.85[AMR][1000 genomes]
rs11716614	0.88[AMR][1000 genomes]
rs11717978	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718982	1.00[AMR][1000 genomes]
rs11719220	0.81[EUR][1000 genomes]
rs11719457	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493001	0.81[ASN][1000 genomes]
rs12636030	0.81[ASN][1000 genomes]
rs12637037	0.92[ASN][1000 genomes]
rs13064784	0.82[ASN][1000 genomes]
rs13064911	0.82[ASN][1000 genomes]
rs13072554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073997	0.85[AMR][1000 genomes]
rs13074318	0.85[AMR][1000 genomes]
rs13084000	0.85[AMR][1000 genomes]
rs13086240	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13087930	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13090839	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes]
rs13096406	0.84[EUR][1000 genomes]
rs13316620	0.84[ASN][1000 genomes]
rs3212	0.82[ASN][1000 genomes]
rs34326553	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34477108	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34504524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34509487	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34566463	0.81[EUR][1000 genomes]
rs34580506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34889065	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35060561	0.81[EUR][1000 genomes]
rs35102816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35108630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35283189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35673421	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3923475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072859	0.89[ASN][1000 genomes]
rs4279134	0.82[ASN][1000 genomes]
rs4364202	0.80[ASN][1000 genomes]
rs4513485	0.82[ASN][1000 genomes]
rs4521268	0.82[ASN][1000 genomes]
rs4974080	0.85[ASN][1000 genomes]
rs5030795	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56004653	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56318350	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61729488	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62262517	0.80[ASN][1000 genomes]
rs6414613	0.85[ASN][1000 genomes]
rs6446196	0.84[ASN][1000 genomes]
rs6446198	0.82[ASN][1000 genomes]
rs6446205	0.85[ASN][1000 genomes]
rs66991555	0.84[EUR][1000 genomes]
rs67060340	0.82[AMR][1000 genomes]
rs67332931	0.85[AMR][1000 genomes]
rs6779394	0.87[ASN][1000 genomes]
rs6781790	0.85[ASN][1000 genomes]
rs6784111	0.81[ASN][1000 genomes]
rs6789285	0.89[ASN][1000 genomes]
rs6795025	1.00[ASN][1000 genomes]
rs71324924	0.85[AMR][1000 genomes]
rs71324929	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73082362	0.88[AMR][1000 genomes]
rs7373790	0.92[ASN][1000 genomes]
rs7430198	0.82[ASN][1000 genomes]
rs7432989	0.90[ASN][1000 genomes]
rs7615235	0.90[ASN][1000 genomes]
rs7626445	0.82[ASN][1000 genomes]
rs7639332	0.82[ASN][1000 genomes]
rs8926	0.90[ASN][1000 genomes]
rs9814987	0.82[EUR][1000 genomes]
rs9835439	0.81[ASN][1000 genomes]
rs9837237	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837625	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9840050	0.82[ASN][1000 genomes]
rs9846123	0.95[ASN][1000 genomes]
rs9855123	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862483	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880088	0.86[EUR][1000 genomes];0.81[ASN][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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13080725	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13080725	WDR6	cis	Adipose Subcutaneous	GTEx
rs13080725	WDR6	cis	Artery Tibial	GTEx
rs13080725	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs13080725	WDR6	cis	Esophagus Mucosa	GTEx
rs13080725	WDR6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49067200-49078600	Weak transcription	Psoas Muscle	Psoas
4	chr3:49067200-49085600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
6	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:49067400-49076400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:49067400-49077200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:49067400-49079800	Strong transcription	Placenta	Placenta
10	chr3:49067400-49085000	Strong transcription	Brain Germinal Matrix	brain
11	chr3:49067400-49085600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:49067400-49085600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:49067400-49085600	Strong transcription	Fetal Intestine Large	intestine
14	chr3:49067400-49086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:49067400-49086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:49067400-49090000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
20	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
21	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
22	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:49067600-49080200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:49067600-49085600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:49067600-49085600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:49067600-49085600	Strong transcription	Liver	Liver
28	chr3:49067600-49086600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:49067600-49086800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:49067600-49095800	Strong transcription	Dnd41	blood
31	chr3:49067600-49097000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
33	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:49067800-49076400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr3:49067800-49086800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:49067800-49086800	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:49068200-49081200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:49070600-49076600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:49070600-49079800	Weak transcription	A549	lung
41	chr3:49070600-49085000	Strong transcription	Adipose Nuclei	Adipose
42	chr3:49070800-49077000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:49070800-49078200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:49070800-49078200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:49070800-49078400	Weak transcription	Colonic Mucosa	Colon
46	chr3:49070800-49079600	Weak transcription	Esophagus	oesophagus
47	chr3:49070800-49083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:49070800-49084600	Strong transcription	Fetal Lung	lung
49	chr3:49070800-49085600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:49070800-49085600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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