Variant report

Variant	rs13068038
Chromosome Location	chr3:49294250-49294251
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49290210..49292392-chr3:49292429..49294964,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10049462	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][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]
rs10154895	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1134043	0.93[CEU][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11706052	0.81[EUR][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11710247	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11716445	0.92[CEU][hapmap]
rs11718982	0.86[EUR][1000 genomes]
rs11719220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11720460	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12493001	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12493284	0.83[ASN][1000 genomes]
rs12629637	0.97[ASN][1000 genomes]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12715434	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072554	0.80[EUR][1000 genomes]
rs13077498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13096406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13321689	1.00[ASW][hapmap]
rs2117938	1.00[JPT][hapmap]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28690891	0.81[AFR][1000 genomes]
rs3212	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34326553	0.87[EUR][1000 genomes]
rs34343820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs34784192	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35060561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35108630	0.81[EUR][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35185152	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs35673421	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4410472	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4955418	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4955419	1.00[JPT][hapmap]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4955432	1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs55921200	0.81[EUR][1000 genomes]
rs56306491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66991555	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67286839	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6779394	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784111	1.00[JPT][hapmap]
rs71324939	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7432989	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7614738	0.83[ASN][1000 genomes]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7638154	0.87[ASN][1000 genomes]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311440	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9818758	0.93[MKK][hapmap];1.00[YRI][hapmap]
rs9826085	1.00[ASW][hapmap]
rs9826525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828310	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835439	0.89[EUR][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9840050	1.00[CHD][hapmap]
rs9844757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9847839	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850917	1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9855123	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9862483	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870030	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9873994	0.93[MKK][hapmap];1.00[YRI][hapmap]
rs9874474	0.86[ASN][1000 genomes]
rs9880088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883409	0.86[ASN][1000 genomes]
rs9990153	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.97[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs13068038	WDR6	cis	Artery Tibial	GTEx
rs13068038	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13068038	WDR6	cis	Esophagus Mucosa	GTEx
rs13068038	CCDC36	cis	cerebellum	SCAN
rs13068038	ALAS1	cis	cerebellum	SCAN
rs13068038	ARIH2	cis	cerebellum	SCAN
rs13068038	CSPG5	cis	parietal	SCAN
rs13068038	C3orf62	cis	cerebellum	SCAN
rs13068038	WDR6	cis	cerebellum	SCAN
rs13068038	WDR6	cis	Adipose Subcutaneous	GTEx
rs13068038	RNF123	cis	parietal	SCAN
rs13068038	NICN1	cis	cerebellum	SCAN
rs13068038	HEMK1	cis	parietal	SCAN
rs13068038	WDR6	cis	Whole Blood	GTEx
rs13068038	LRRC2	cis	cerebellum	SCAN
rs13068038	WDR6	cis	parietal	SCAN
rs13068038	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs13068038	KBTBD3	trans	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49276400-49306400	Weak transcription	Spleen	Spleen
2	chr3:49276600-49304000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:49282600-49294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:49282600-49299000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:49282600-49303200	Weak transcription	Left Ventricle	heart
6	chr3:49286400-49304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:49286400-49313600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:49290600-49303400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:49291200-49294400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49292200-49295400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:49292600-49294400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:49292600-49295000	Enhancers	Colon Smooth Muscle	Colon
13	chr3:49292600-49295000	Enhancers	Fetal Intestine Large	intestine
14	chr3:49292600-49295000	Enhancers	Fetal Intestine Small	intestine
15	chr3:49292600-49295000	Strong transcription	Fetal Stomach	stomach
16	chr3:49292800-49306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:49293000-49313400	Weak transcription	HSMM	muscle
18	chr3:49293200-49294400	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr3:49293200-49294600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:49293200-49294600	Genic enhancers	Fetal Muscle Leg	muscle
21	chr3:49293200-49294800	Genic enhancers	Adipose Nuclei	Adipose
22	chr3:49293200-49295000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:49293200-49295200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:49293400-49294400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:49293400-49294800	Strong transcription	NHLF	lung
26	chr3:49293400-49295000	Enhancers	Rectal Smooth Muscle	rectum
27	chr3:49293400-49295000	Strong transcription	Osteobl	bone
28	chr3:49293600-49294400	Enhancers	Right Atrium	heart
29	chr3:49293600-49294600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:49293600-49295000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:49293600-49295000	Strong transcription	Right Ventricle	heart
32	chr3:49293600-49304000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:49293600-49306400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:49293800-49294400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:49293800-49295000	Enhancers	Ovary	ovary
36	chr3:49293800-49305400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:49293800-49306400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr3:49293800-49307000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:49293800-49308400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:49294000-49294600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:49294000-49296400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:49294000-49306600	Weak transcription	Placenta	Placenta
43	chr3:49294000-49308400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:49294200-49294600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:49294200-49297600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:49294200-49303400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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