Variant report

Variant	rs9828310
Chromosome Location	chr3:49289387-49289388
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10049462	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10154895	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11552724	0.91[EUR][1000 genomes]
rs11706052	0.81[EUR][1000 genomes]
rs11706189	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11710247	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11713297	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11718982	0.86[EUR][1000 genomes]
rs11719220	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11720460	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12493284	0.83[ASN][1000 genomes]
rs12629637	0.97[ASN][1000 genomes]
rs12715434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12715435	0.81[AFR][1000 genomes]
rs13068038	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072554	0.80[EUR][1000 genomes]
rs13077498	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13096406	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2304442	0.86[ASN][1000 genomes]
rs34326553	0.87[EUR][1000 genomes]
rs34343820	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566463	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34784192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35060561	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35108630	0.81[EUR][1000 genomes]
rs35174559	0.92[ASN][1000 genomes]
rs35185152	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35673421	0.89[EUR][1000 genomes]
rs4410472	0.91[ASN][1000 genomes]
rs5030795	0.91[EUR][1000 genomes]
rs55921200	0.81[EUR][1000 genomes]
rs56306491	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66991555	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67286839	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67831908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324939	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7614738	0.83[ASN][1000 genomes]
rs7638154	0.87[ASN][1000 genomes]
rs9311439	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814987	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9826525	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9835439	0.89[EUR][1000 genomes]
rs9837237	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9837625	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9847839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9855123	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9862483	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870030	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9874474	0.86[ASN][1000 genomes]
rs9880088	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9880309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883409	0.86[ASN][1000 genomes]
rs9990153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9828310	WDR6	cis	Whole Blood	GTEx
rs9828310	WDR6	cis	Esophagus Mucosa	GTEx
rs9828310	WDR6	cis	Artery Tibial	GTEx
rs9828310	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9828310	WDR6	cis	Adipose Subcutaneous	GTEx
rs9828310	USP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49266200-49292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:49276400-49293400	Weak transcription	NHLF	lung
3	chr3:49276400-49306400	Weak transcription	Spleen	Spleen
4	chr3:49276600-49304000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:49277400-49292600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:49282600-49294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:49282600-49299000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:49282600-49303200	Weak transcription	Left Ventricle	heart
9	chr3:49283400-49293200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:49285200-49292600	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:49285200-49292600	Weak transcription	Fetal Stomach	stomach
12	chr3:49285200-49293200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:49286400-49292600	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:49286400-49304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:49286400-49313600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:49286600-49292800	Weak transcription	NHDF-Ad	bronchial
17	chr3:49286600-49293200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:49286600-49293200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:49286600-49293600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:49286600-49293600	Weak transcription	Right Ventricle	heart
21	chr3:49286600-49293800	Weak transcription	Ovary	ovary
22	chr3:49286600-49294000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:49286800-49292200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:49287200-49292600	Weak transcription	Adipose Nuclei	Adipose
25	chr3:49287200-49293600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:49287400-49292000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:49287400-49292400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:49287400-49293600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:49288000-49293400	Weak transcription	Osteobl	bone
30	chr3:49288200-49290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:49288200-49290800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:49288200-49292400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:49288200-49292400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:49288400-49292200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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