Variant report

Variant	rs11719457
Chromosome Location	chr3:48974385-48974386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48970141..48972783-chr3:48973046..48975012,2	K562	blood:
2	chr3:48954704..48957536-chr3:48971085..48974504,3	K562	blood:
3	chr3:48955222..48958989-chr3:48973155..48975236,3	MCF-7	breast:
4	chr3:48962905..48965983-chr3:48972430..48974788,3	K562	blood:
5	chr3:48954892..48957372-chr3:48974125..48976398,2	K562	blood:
6	chr3:48963303..48970109-chr3:48970555..48975034,7	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf71-1	chr3:48974021-48976346	ENSG00000246870
2	lnc-C3orf71-1	chr3:48974258-48975090	ENSG00000246870

No data

Variant related genes	Relation type
ENSG00000177479	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10154895	0.82[EUR][1000 genomes]
rs1048940	0.82[AMR][1000 genomes]
rs10780033	0.90[ASN][1000 genomes]
rs11130176	0.90[ASN][1000 genomes]
rs1134591	0.95[ASN][1000 genomes]
rs11552724	0.85[EUR][1000 genomes]
rs11557629	0.80[AMR][1000 genomes]
rs11705737	0.95[ASN][1000 genomes]
rs11706052	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11706189	0.81[EUR][1000 genomes]
rs11706203	0.80[AMR][1000 genomes]
rs11706983	0.80[AMR][1000 genomes]
rs11708022	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709092	0.85[AMR][1000 genomes]
rs11709246	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712006	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11712982	0.97[ASN][1000 genomes]
rs11713297	0.81[EUR][1000 genomes]
rs11713694	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715689	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11715713	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11715835	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11717978	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718982	0.89[AMR][1000 genomes]
rs11719291	0.80[AMR][1000 genomes]
rs11920534	0.97[ASN][1000 genomes]
rs11924597	0.97[ASN][1000 genomes]
rs12493289	0.85[ASN][1000 genomes]
rs12637037	0.80[ASN][1000 genomes]
rs13064911	1.00[ASN][1000 genomes]
rs13072554	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13072911	0.95[ASN][1000 genomes]
rs13073997	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074318	0.89[AMR][1000 genomes]
rs13076394	0.84[ASN][1000 genomes]
rs13080725	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13084000	0.89[AMR][1000 genomes]
rs13086240	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13087930	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090013	0.80[AMR][1000 genomes]
rs13090839	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13094900	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13096406	0.81[EUR][1000 genomes]
rs13315711	0.95[ASN][1000 genomes]
rs13316551	0.80[AMR][1000 genomes]
rs13316620	0.87[ASN][1000 genomes]
rs13434258	0.80[AMR][1000 genomes]
rs17080319	0.80[AMR][1000 genomes]
rs28567949	0.80[AMR][1000 genomes]
rs28642807	0.95[ASN][1000 genomes]
rs28657585	0.80[AMR][1000 genomes]
rs34037363	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34153629	0.80[AMR][1000 genomes]
rs34326553	0.81[EUR][1000 genomes]
rs34477108	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34504524	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34509487	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34580506	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34889065	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35064573	0.80[AMR][1000 genomes]
rs35102816	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35108630	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35283189	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35673421	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3923475	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4072859	0.92[ASN][1000 genomes]
rs4974078	0.88[ASN][1000 genomes]
rs4974079	0.95[ASN][1000 genomes]
rs4974080	0.87[ASN][1000 genomes]
rs4974082	0.92[ASN][1000 genomes]
rs4974084	0.97[ASN][1000 genomes]
rs4974085	0.90[ASN][1000 genomes]
rs4974087	0.90[ASN][1000 genomes]
rs5030795	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55674449	0.93[ASN][1000 genomes]
rs56318350	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61729488	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6414613	0.87[ASN][1000 genomes]
rs6446196	0.97[ASN][1000 genomes]
rs6446198	0.95[ASN][1000 genomes]
rs6446205	0.87[ASN][1000 genomes]
rs6446252	0.90[ASN][1000 genomes]
rs6446253	0.85[ASN][1000 genomes]
rs66991555	0.81[EUR][1000 genomes]
rs67060340	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67332931	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6768433	0.81[ASN][1000 genomes]
rs6781790	0.87[ASN][1000 genomes]
rs6786665	0.95[ASN][1000 genomes]
rs6791234	0.95[ASN][1000 genomes]
rs6795025	0.82[ASN][1000 genomes]
rs71324924	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71324929	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73078349	0.85[AMR][1000 genomes]
rs73078362	0.85[AMR][1000 genomes]
rs73080312	0.82[AMR][1000 genomes]
rs7373778	0.92[ASN][1000 genomes]
rs7430198	1.00[ASN][1000 genomes]
rs7430501	0.90[ASN][1000 genomes]
rs7431710	0.95[ASN][1000 genomes]
rs7431857	0.90[ASN][1000 genomes]
rs7612459	0.90[ASN][1000 genomes]
rs7623023	0.90[ASN][1000 genomes]
rs7627404	0.87[ASN][1000 genomes]
rs7628719	0.95[ASN][1000 genomes]
rs7636057	0.82[ASN][1000 genomes]
rs7639332	1.00[ASN][1000 genomes]
rs7643368	0.95[ASN][1000 genomes]
rs7649458	0.90[ASN][1000 genomes]
rs8926	0.82[ASN][1000 genomes]
rs9311430	0.90[ASN][1000 genomes]
rs9311432	0.90[ASN][1000 genomes]
rs9311433	0.90[ASN][1000 genomes]
rs9311434	0.85[ASN][1000 genomes]
rs9681717	0.95[ASN][1000 genomes]
rs9682444	0.92[ASN][1000 genomes]
rs9754878	0.92[ASN][1000 genomes]
rs9755490	0.95[ASN][1000 genomes]
rs9811027	0.80[AMR][1000 genomes]
rs9814987	0.80[EUR][1000 genomes]
rs9830636	0.90[ASN][1000 genomes]
rs9835307	0.95[ASN][1000 genomes]
rs9837237	0.81[EUR][1000 genomes]
rs9837625	0.81[EUR][1000 genomes]
rs9840684	0.90[ASN][1000 genomes]
rs9850134	0.95[ASN][1000 genomes]
rs9855123	0.81[EUR][1000 genomes]
rs9862483	0.81[EUR][1000 genomes]
rs9867373	0.95[ASN][1000 genomes]
rs9876848	0.90[ASN][1000 genomes]
rs9879971	0.90[ASN][1000 genomes]
rs9880088	0.84[EUR][1000 genomes]
rs9884022	0.95[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11719457	WDR6	cis	Esophagus Mucosa	GTEx
rs11719457	WDR6	cis	Whole Blood	GTEx
rs11719457	WDR6	cis	Artery Tibial	GTEx
rs11719457	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11719457	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48957400-49003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48957600-48974400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:48959000-48976000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48959000-48976200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:48959400-48976200	Strong transcription	Fetal Thymus	thymus
6	chr3:48959600-48975800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:48962000-49000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:48965200-49004200	Weak transcription	Colonic Mucosa	Colon
9	chr3:48965400-48981200	Weak transcription	Right Ventricle	heart
10	chr3:48965400-49000000	Weak transcription	Esophagus	oesophagus
11	chr3:48965800-48995400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:48965800-49000000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:48965800-49004000	Weak transcription	Fetal Brain Male	brain
14	chr3:48966000-48986000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:48966000-49008000	Weak transcription	Fetal Kidney	kidney
16	chr3:48966400-48975800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:48966600-48986200	Weak transcription	NHLF	lung
18	chr3:48966800-48986200	Weak transcription	HMEC	breast
19	chr3:48967200-48977200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:48967200-48980800	Weak transcription	Aorta	Aorta
21	chr3:48967400-48994800	Weak transcription	Gastric	stomach
22	chr3:48967600-48983400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:48968000-48997200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:48968200-48976200	Weak transcription	Small Intestine	intestine
25	chr3:48968200-48997200	Weak transcription	NHDF-Ad	bronchial
26	chr3:48969400-48975000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr3:48970200-48974600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:48970400-48975200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:48970400-48975200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:48970400-48977000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:48970400-48982200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:48970400-48982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:48970400-48982400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:48970400-48984000	Weak transcription	Brain Angular Gyrus	brain
35	chr3:48970400-49004400	Weak transcription	Pancreas	Pancrea
36	chr3:48970600-48975800	Strong transcription	GM12878-XiMat	blood
37	chr3:48970600-48991600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:48970800-48976200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:48970800-48976200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:48970800-48986600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:48970800-48991000	Weak transcription	Lung	lung
42	chr3:48970800-49002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:48971000-48975200	Strong transcription	HSMM	muscle
44	chr3:48971000-48975400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:48971000-48982200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:48971000-48994800	Weak transcription	Spleen	Spleen
47	chr3:48971200-48975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:48971400-48975200	Strong transcription	HUVEC	blood vessel
49	chr3:48971400-48980600	Weak transcription	Fetal Stomach	stomach
50	chr3:48971400-48986200	Weak transcription	Brain Anterior Caudate	brain

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