Variant report

Variant	rs13072911
Chromosome Location	chr3:48962128-48962129
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48955220..48957658-chr3:48960315..48963071,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177479	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10780033	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130176	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134591	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705737	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705888	0.83[EUR][1000 genomes]
rs11708022	0.85[ASN][1000 genomes]
rs11709246	0.90[ASN][1000 genomes]
rs11712982	0.92[ASN][1000 genomes]
rs11713694	0.87[ASN][1000 genomes]
rs11717978	0.95[ASN][1000 genomes]
rs11719457	0.95[ASN][1000 genomes]
rs11920534	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11924597	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491743	0.84[EUR][1000 genomes]
rs12493289	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12637037	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13064784	0.81[EUR][1000 genomes]
rs13064883	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064911	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13073997	0.90[ASN][1000 genomes]
rs13076394	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13078308	0.87[EUR][1000 genomes]
rs13086240	0.92[ASN][1000 genomes]
rs13087930	0.95[ASN][1000 genomes]
rs13090839	0.92[ASN][1000 genomes]
rs13094900	0.87[ASN][1000 genomes]
rs13315711	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13316620	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28642807	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34477108	0.95[ASN][1000 genomes]
rs34504524	0.87[ASN][1000 genomes]
rs34509487	0.95[ASN][1000 genomes]
rs3774628	0.82[EUR][1000 genomes]
rs4072859	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974078	0.88[ASN][1000 genomes]
rs4974079	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974080	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974082	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974084	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974085	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974087	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974091	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55674449	0.88[ASN][1000 genomes]
rs56318350	0.95[ASN][1000 genomes]
rs6414613	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446196	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446198	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446205	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446252	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446253	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67060340	0.90[ASN][1000 genomes]
rs67332931	0.90[ASN][1000 genomes]
rs6768433	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6781790	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6786665	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6789285	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6791234	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795025	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71324924	0.90[ASN][1000 genomes]
rs7372149	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7373778	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7373790	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7430198	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7430501	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431710	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431857	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7432989	0.85[EUR][1000 genomes]
rs7612459	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615235	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7615675	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7621015	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7623023	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626445	0.87[EUR][1000 genomes]
rs7627404	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7628719	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636057	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7639332	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643368	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647093	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7649458	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8926	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9311430	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311432	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311433	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311434	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9681717	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9682444	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9754878	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9755490	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9830636	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835307	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9840050	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9840684	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846123	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9850134	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867373	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876848	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879971	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9884022	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs13072911	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs13072911	NICN1	cis	Thyroid	GTEx
rs13072911	WDR6	cis	Muscle Skeletal	GTEx
rs13072911	WDR6	cis	Artery Tibial	GTEx
rs13072911	WDR6	cis	Nerve Tibial	GTEx
rs13072911	AMT	cis	Artery Aorta	GTEx
rs13072911	NCKIPSD	cis	Whole Blood	GTEx
rs13072911	WDR6	cis	Adipose Subcutaneous	GTEx
rs13072911	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs13072911	WDR6	cis	Heart Left Ventricle	GTEx
rs13072911	WDR6	cis	lung	GTEx
rs13072911	CCDC36	cis	Artery Tibial	GTEx
rs13072911	AMT	cis	Thyroid	GTEx
rs13072911	NCKIPSD	cis	Nerve Tibial	GTEx
rs13072911	WDR6	cis	Esophagus Mucosa	GTEx
rs13072911	NICN1-AS1	cis	Thyroid	GTEx
rs13072911	WDR6	cis	Whole Blood	GTEx
rs13072911	WDR6	cis	Esophagus Muscularis	GTEx
rs13072911	NCKIPSD	cis	Muscle Skeletal	GTEx
rs13072911	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs13072911	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48957200-48965000	Weak transcription	Small Intestine	intestine
2	chr3:48957400-49003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48957600-48964400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:48957600-48964400	Weak transcription	HSMMtube	muscle
5	chr3:48957600-48965000	Weak transcription	Fetal Kidney	kidney
6	chr3:48957600-48974400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:48957800-48963000	Weak transcription	NHDF-Ad	bronchial
8	chr3:48957800-48963400	Weak transcription	HSMM	muscle
9	chr3:48957800-48964000	Weak transcription	HMEC	breast
10	chr3:48957800-48964600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:48957800-48964600	Weak transcription	Aorta	Aorta
12	chr3:48957800-48965000	Weak transcription	Right Ventricle	heart
13	chr3:48958000-48963600	Weak transcription	A549	lung
14	chr3:48958000-48964400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:48958000-48964400	Weak transcription	Stomach Mucosa	stomach
16	chr3:48958000-48965000	Weak transcription	Fetal Brain Male	brain
17	chr3:48958400-48964000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:48958800-48965400	Strong transcription	Fetal Intestine Small	intestine
19	chr3:48959000-48965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:48959000-48965200	Strong transcription	Fetal Stomach	stomach
21	chr3:48959000-48968400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:48959000-48971600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:48959000-48974000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:48959000-48976000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:48959000-48976200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:48959200-48962200	Strong transcription	Fetal Lung	lung
27	chr3:48959200-48962800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:48959200-48963800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:48959200-48964000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:48959200-48964200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:48959200-48964800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:48959200-48965000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr3:48959200-48968200	Strong transcription	Thymus	Thymus
34	chr3:48959200-48971000	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:48959200-48973600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:48959400-48962200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:48959400-48963200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:48959400-48964000	Strong transcription	Spleen	Spleen
39	chr3:48959400-48964600	Weak transcription	Gastric	stomach
40	chr3:48959400-48965400	Strong transcription	Brain Germinal Matrix	brain
41	chr3:48959400-48968200	Strong transcription	Fetal Intestine Large	intestine
42	chr3:48959400-48976200	Strong transcription	Fetal Thymus	thymus
43	chr3:48959600-48962800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:48959600-48963000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:48959600-48963000	Weak transcription	Brain Substantia Nigra	brain
46	chr3:48959600-48963800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:48959600-48964000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:48959600-48964200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:48959600-48964200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr3:48959600-48964200	Strong transcription	Monocytes-CD14+_RO01746	blood

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