Variant report

Variant	rs9880309
Chromosome Location	chr3:49304329-49304330
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10154895	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10865954	1.00[JPT][hapmap]
rs11130184	1.00[JPT][hapmap]
rs1134043	0.91[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11710247	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11715581	1.00[JPT][hapmap]
rs11716445	0.90[CEU][hapmap]
rs11718982	0.81[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11720460	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12490393	1.00[JPT][hapmap]
rs12493001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12493284	0.83[ASN][1000 genomes]
rs12629637	0.97[ASN][1000 genomes]
rs12629759	1.00[JPT][hapmap]
rs12631989	1.00[JPT][hapmap]
rs12637576	1.00[JPT][hapmap]
rs12715434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715435	0.81[AFR][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13096406	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17080505	1.00[JPT][hapmap]
rs2117938	1.00[JPT][hapmap]
rs2304442	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2334956	1.00[JPT][hapmap]
rs3212	1.00[JPT][hapmap]
rs34326553	0.82[EUR][1000 genomes]
rs34343820	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs34784192	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35060561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35174559	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35185152	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35220094	1.00[JPT][hapmap]
rs35260967	1.00[JPT][hapmap]
rs35283189	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs35673421	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4279134	1.00[JPT][hapmap]
rs4410472	0.91[ASN][1000 genomes]
rs4513485	1.00[JPT][hapmap]
rs4521268	1.00[JPT][hapmap]
rs4955410	1.00[JPT][hapmap]
rs4955418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955419	1.00[JPT][hapmap]
rs4955420	1.00[JPT][hapmap]
rs4955432	1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs56306491	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66991555	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67286839	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6779394	1.00[JPT][hapmap]
rs67831908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784111	1.00[CHB][hapmap]
rs71324939	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73084135	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7614738	0.83[ASN][1000 genomes]
rs7626445	1.00[JPT][hapmap]
rs7638154	0.87[ASN][1000 genomes]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9826525	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9828310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835439	0.87[EUR][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9844757	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9847839	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850917	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9855123	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9862483	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9870030	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9874474	0.86[ASN][1000 genomes]
rs9880088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9883409	0.86[ASN][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv963481	chr3:49304260-49325571	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9880309	WDR6	cis	Esophagus Mucosa	GTEx
rs9880309	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9880309	WDR6	cis	Adipose Subcutaneous	GTEx
rs9880309	WDR6	cis	Artery Tibial	GTEx
rs9880309	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9880309	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49276400-49306400	Weak transcription	Spleen	Spleen
2	chr3:49286400-49313600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:49292800-49306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:49293000-49313400	Weak transcription	HSMM	muscle
5	chr3:49293600-49306400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:49293800-49305400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:49293800-49306400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:49293800-49307000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:49293800-49308400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:49294000-49306600	Weak transcription	Placenta	Placenta
11	chr3:49294000-49308400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:49294800-49306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:49294800-49313400	Weak transcription	NHLF	lung
14	chr3:49295000-49306600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49295000-49313200	Weak transcription	Right Ventricle	heart
16	chr3:49298400-49307000	Weak transcription	Lung	lung
17	chr3:49299000-49313600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:49299400-49306400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:49299400-49306600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:49299400-49307000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:49300200-49306600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:49300200-49313400	Weak transcription	HUVEC	blood vessel
23	chr3:49300800-49307000	Weak transcription	Aorta	Aorta
24	chr3:49301200-49306800	Weak transcription	Fetal Brain Female	brain
25	chr3:49301600-49306600	Weak transcription	Primary B cells from cord blood	blood
26	chr3:49301800-49306600	Weak transcription	Gastric	stomach
27	chr3:49301800-49306600	Weak transcription	Dnd41	blood
28	chr3:49301800-49315600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49302000-49307000	Weak transcription	Thymus	Thymus
30	chr3:49302200-49306600	Weak transcription	Fetal Thymus	thymus
31	chr3:49302200-49308600	Enhancers	Fetal Intestine Large	intestine
32	chr3:49302200-49311800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:49302800-49306200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:49302800-49313400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:49303000-49306600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:49303200-49304800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:49303200-49304800	Enhancers	Left Ventricle	heart
38	chr3:49303200-49305000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr3:49303400-49304400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:49303400-49304800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:49303400-49304800	Enhancers	Colon Smooth Muscle	Colon
42	chr3:49303400-49305000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:49303400-49305000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:49303400-49305000	Enhancers	Brain Angular Gyrus	brain
45	chr3:49303400-49305000	Enhancers	Brain Cingulate Gyrus	brain
46	chr3:49303400-49305000	Enhancers	Fetal Muscle Leg	muscle
47	chr3:49303400-49305000	Enhancers	Right Atrium	heart
48	chr3:49303400-49305000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:49303400-49305600	Enhancers	Ovary	ovary
50	chr3:49303400-49306400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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