Variant report

Variant	rs11712006
Chromosome Location	chr3:49115948-49115949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49044904..49047427-chr3:49115709..49117786,2	MCF-7	breast:
2	chr3:49113907..49116701-chr3:49123584..49125304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178252	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10154895	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865954	0.85[ASN][1000 genomes]
rs11130184	0.82[ASN][1000 genomes]
rs11552724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706189	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11708022	0.85[AMR][1000 genomes]
rs11709092	0.81[AMR][1000 genomes]
rs11709246	0.85[AMR][1000 genomes]
rs11713297	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713694	0.85[AMR][1000 genomes]
rs11715581	0.82[ASN][1000 genomes]
rs11716334	0.82[ASN][1000 genomes]
rs11716614	0.88[AMR][1000 genomes]
rs11717978	0.86[EUR][1000 genomes]
rs11718982	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11719457	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12487580	0.80[ASN][1000 genomes]
rs12490393	0.82[ASN][1000 genomes]
rs12493001	0.89[ASN][1000 genomes]
rs12629759	0.82[ASN][1000 genomes]
rs12636030	0.89[ASN][1000 genomes]
rs12637037	0.80[ASN][1000 genomes]
rs12637576	0.82[ASN][1000 genomes]
rs13064784	0.95[ASN][1000 genomes]
rs13072554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][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];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086240	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13087930	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13090839	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes]
rs13096406	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3212	0.95[ASN][1000 genomes]
rs34326553	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34477108	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34504524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34509487	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34580506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889065	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35102816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35108630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35283189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35673421	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4279134	0.95[ASN][1000 genomes]
rs4308307	0.82[ASN][1000 genomes]
rs4364202	0.93[ASN][1000 genomes]
rs4499638	0.87[ASN][1000 genomes]
rs4513485	0.95[ASN][1000 genomes]
rs4521268	0.95[ASN][1000 genomes]
rs4536858	0.87[ASN][1000 genomes]
rs4955410	0.85[ASN][1000 genomes]
rs4955418	0.87[ASN][1000 genomes]
rs4955419	0.82[ASN][1000 genomes]
rs4955420	0.82[ASN][1000 genomes]
rs5030795	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55713230	0.87[ASN][1000 genomes]
rs56004653	0.88[AMR][1000 genomes]
rs56318350	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61583136	0.85[ASN][1000 genomes]
rs61729488	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62262517	0.93[ASN][1000 genomes]
rs66991555	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67060340	0.82[AMR][1000 genomes]
rs67332931	0.85[AMR][1000 genomes]
rs6770112	0.85[ASN][1000 genomes]
rs6779394	1.00[ASN][1000 genomes]
rs6784111	0.89[ASN][1000 genomes]
rs6790914	0.87[ASN][1000 genomes]
rs6794924	0.82[ASN][1000 genomes]
rs6795025	0.87[ASN][1000 genomes]
rs71324924	0.85[AMR][1000 genomes]
rs71324929	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73082362	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7615235	0.87[ASN][1000 genomes]
rs7626445	0.95[ASN][1000 genomes]
rs9814987	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835439	0.89[ASN][1000 genomes]
rs9837237	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837625	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840050	0.95[ASN][1000 genomes]
rs9846123	0.82[ASN][1000 genomes]
rs9855123	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862483	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880088	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv3351308	chr3:49115759-49116174	Strong transcription Genic enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11712006	WDR6	cis	Esophagus Mucosa	GTEx
rs11712006	WDR6	cis	Adipose Subcutaneous	GTEx
rs11712006	WDR6	cis	Artery Tibial	GTEx
rs11712006	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11712006	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:126 , 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	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
7	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
8	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
9	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
12	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:49070800-49117000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:49073400-49118200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:49077400-49117200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:49084600-49117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:49087800-49117600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:49088000-49116800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:49088000-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:49088000-49118400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:49088200-49116800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr3:49088400-49116800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:49088600-49116400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:49088600-49116800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:49088600-49116800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:49094600-49128200	Weak transcription	Fetal Brain Male	brain
28	chr3:49095000-49117000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:49095200-49117200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:49095400-49129600	Weak transcription	Stomach Mucosa	stomach
31	chr3:49096400-49116800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:49096800-49116800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:49096800-49116800	Strong transcription	Placenta	Placenta
34	chr3:49096800-49117200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:49097200-49117200	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:49097800-49118200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:49097800-49118200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:49098000-49116000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr3:49098000-49116800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:49098000-49116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:49098000-49116800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:49098000-49116800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:49098000-49117000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:49098000-49117400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr3:49098000-49117800	Strong transcription	Dnd41	blood
46	chr3:49098200-49116000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:49099200-49117200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:49100600-49117000	Strong transcription	Left Ventricle	heart
49	chr3:49100600-49117400	Strong transcription	Fetal Lung	lung
50	chr3:49101200-49117600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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