Variant report

Variant	rs13072554
Chromosome Location	chr3:49087211-49087212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10154895	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11552724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706189	0.85[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	0.83[EUR][1000 genomes]
rs11712006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713297	0.85[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	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718982	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11719220	0.83[EUR][1000 genomes]
rs11719457	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11720460	0.80[EUR][1000 genomes]
rs12493001	0.81[ASN][1000 genomes]
rs12636030	0.81[ASN][1000 genomes]
rs12637037	0.92[ASN][1000 genomes]
rs12715434	0.80[EUR][1000 genomes]
rs13064784	0.82[ASN][1000 genomes]
rs13064911	0.82[ASN][1000 genomes]
rs13068038	0.80[EUR][1000 genomes]
rs13073997	0.85[AMR][1000 genomes]
rs13074318	0.85[AMR][1000 genomes]
rs13080725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084000	0.85[AMR][1000 genomes]
rs13086240	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13087930	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13090839	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes]
rs13096406	0.85[EUR][1000 genomes]
rs13316620	0.84[ASN][1000 genomes]
rs3212	0.82[ASN][1000 genomes]
rs34326553	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34477108	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34504524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34509487	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34566463	0.83[EUR][1000 genomes]
rs34580506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34784192	0.80[EUR][1000 genomes]
rs34889065	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35060561	0.83[EUR][1000 genomes]
rs35102816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35108630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35185152	0.80[EUR][1000 genomes]
rs35283189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35673421	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3923475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56004653	0.88[AMR][1000 genomes]
rs56318350	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61729488	1.00[AMR][1000 genomes];0.92[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	0.85[EUR][1000 genomes]
rs67060340	0.82[AMR][1000 genomes]
rs67286839	0.80[EUR][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];0.92[EUR][1000 genomes]
rs71324939	0.80[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	0.84[EUR][1000 genomes]
rs9826525	0.80[EUR][1000 genomes]
rs9828310	0.80[EUR][1000 genomes]
rs9835439	0.81[ASN][1000 genomes]
rs9837237	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837625	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9840050	0.82[ASN][1000 genomes]
rs9846123	0.95[ASN][1000 genomes]
rs9847839	0.80[EUR][1000 genomes]
rs9850917	0.80[EUR][1000 genomes]
rs9855123	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862483	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880088	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9990153	0.80[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	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
rs13072554	WDR6	cis	Whole Blood	GTEx
rs13072554	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs13072554	WDR6	cis	Adipose Subcutaneous	GTEx
rs13072554	WDR6	cis	Esophagus Mucosa	GTEx
rs13072554	WDR6	cis	Artery Tibial	GTEx
rs13072554	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	chr3:49066800-49130000	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	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
4	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:49067400-49090000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
9	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
10	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
11	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:49067600-49095800	Strong transcription	Dnd41	blood
14	chr3:49067600-49097000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
16	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:49070800-49117000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:49072400-49094200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:49073400-49118200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:49074200-49096000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:49077400-49117200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:49078800-49091200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:49082600-49091800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:49084400-49088600	Weak transcription	K562	blood
26	chr3:49084400-49094000	Weak transcription	Psoas Muscle	Psoas
27	chr3:49084600-49088000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:49084600-49088200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:49084600-49088200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:49084600-49088200	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:49084600-49088200	Weak transcription	NHLF	lung
32	chr3:49084600-49088400	Weak transcription	Pancreas	Pancrea
33	chr3:49084600-49088800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:49084600-49089000	Weak transcription	Fetal Lung	lung
35	chr3:49084600-49089200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:49084600-49089200	Weak transcription	Aorta	Aorta
37	chr3:49084600-49089400	Weak transcription	Fetal Brain Male	brain
38	chr3:49084600-49091000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:49084600-49091000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:49084600-49091200	Weak transcription	Fetal Kidney	kidney
41	chr3:49084600-49091400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:49084600-49093800	Weak transcription	Stomach Mucosa	stomach
43	chr3:49084600-49094000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:49084600-49094000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr3:49084600-49110800	Weak transcription	Fetal Heart	heart
46	chr3:49084600-49117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:49084800-49087800	Weak transcription	Hela-S3	cervix
48	chr3:49084800-49088200	Weak transcription	Brain Anterior Caudate	brain
49	chr3:49084800-49088200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:49084800-49088200	Weak transcription	Rectal Mucosa Donor 29	rectum

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