Variant report

Variant	rs7373790
Chromosome Location	chr3:49090696-49090697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49083063..49085936-chr3:49089471..49091268,3	MCF-7	breast:
2	chr3:49087875..49089929-chr3:49090268..49092361,2	K562	blood:
3	chr3:49088204..49092295-chr3:49137425..49140867,4	MCF-7	breast:
4	chr3:49057987..49061748-chr3:49089649..49091430,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178149	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000172053	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10780033	0.85[EUR][1000 genomes]
rs11130176	0.83[EUR][1000 genomes]
rs11130181	0.87[AFR][1000 genomes]
rs1134591	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11705737	0.91[EUR][1000 genomes]
rs11706052	0.92[ASN][1000 genomes]
rs11920534	0.89[EUR][1000 genomes]
rs11924597	0.89[EUR][1000 genomes]
rs12491743	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12493289	0.85[EUR][1000 genomes]
rs12637037	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13064784	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13064883	0.89[EUR][1000 genomes]
rs13064911	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13072554	0.92[ASN][1000 genomes]
rs13072911	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13076394	0.91[EUR][1000 genomes]
rs13080725	0.92[ASN][1000 genomes]
rs13315711	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13316620	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28642807	0.86[EUR][1000 genomes]
rs3212	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34504524	0.81[ASN][1000 genomes]
rs35102816	0.83[ASN][1000 genomes]
rs35108630	0.92[ASN][1000 genomes]
rs3923475	0.92[ASN][1000 genomes]
rs4072859	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279134	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4292260	0.86[AFR][1000 genomes]
rs4364202	0.86[AMR][1000 genomes]
rs4521268	0.88[AMR][1000 genomes]
rs4955411	0.86[AFR][1000 genomes]
rs4955416	0.90[AFR][1000 genomes]
rs4974079	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4974080	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4974082	0.92[EUR][1000 genomes]
rs4974084	0.85[EUR][1000 genomes]
rs4974085	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4974087	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4974091	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62262517	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6414613	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6446196	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446198	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6446205	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6446252	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6446253	0.85[EUR][1000 genomes]
rs6768433	0.88[EUR][1000 genomes]
rs6779394	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6781790	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6786665	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6789285	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6791234	0.90[EUR][1000 genomes]
rs6795025	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7372149	0.87[EUR][1000 genomes]
rs7373778	0.82[EUR][1000 genomes]
rs7430198	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7430501	0.85[EUR][1000 genomes]
rs7431710	0.88[EUR][1000 genomes]
rs7431857	0.85[EUR][1000 genomes]
rs7432989	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612459	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7615235	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7615675	0.87[EUR][1000 genomes]
rs7617480	0.83[AFR][1000 genomes]
rs7621015	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7623023	0.85[EUR][1000 genomes]
rs7626445	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7627404	0.83[EUR][1000 genomes]
rs7628719	0.92[EUR][1000 genomes]
rs7636057	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7639332	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7643368	0.91[EUR][1000 genomes]
rs7647093	0.87[EUR][1000 genomes]
rs7649458	0.84[EUR][1000 genomes]
rs8926	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311430	0.83[EUR][1000 genomes]
rs9311432	0.83[EUR][1000 genomes]
rs9311433	0.83[EUR][1000 genomes]
rs9311434	0.84[EUR][1000 genomes]
rs9681717	0.85[EUR][1000 genomes]
rs9682444	0.83[EUR][1000 genomes]
rs9754878	0.85[EUR][1000 genomes]
rs9755490	0.85[EUR][1000 genomes]
rs9830636	0.81[EUR][1000 genomes]
rs9835307	0.83[EUR][1000 genomes]
rs9840050	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9840684	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9841640	0.86[EUR][1000 genomes]
rs9846123	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850134	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9867373	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9876848	0.83[EUR][1000 genomes]
rs9879971	0.85[EUR][1000 genomes]
rs9884022	0.82[AMR][1000 genomes];0.91[EUR][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	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

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs7373790	WDR6	cis	lung	GTEx
rs7373790	WDR6	cis	Nerve Tibial	GTEx
rs7373790	WDR6	cis	Heart Left Ventricle	GTEx
rs7373790	AMT	cis	Muscle Skeletal	GTEx
rs7373790	NCKIPSD	cis	Muscle Skeletal	GTEx
rs7373790	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7373790	NCKIPSD	cis	Nerve Tibial	GTEx
rs7373790	WDR6	cis	Artery Tibial	GTEx
rs7373790	WDR6	cis	Esophagus Muscularis	GTEx
rs7373790	WDR6	cis	Muscle Skeletal	GTEx
rs7373790	WDR6	cis	Stomach	GTEx
rs7373790	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7373790	CCDC36	cis	Artery Tibial	GTEx
rs7373790	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7373790	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7373790	WDR6	cis	Esophagus Mucosa	GTEx
rs7373790	AMT	cis	Thyroid	GTEx
rs7373790	NICN1	cis	Thyroid	GTEx
rs7373790	WDR6	cis	Whole Blood	GTEx
rs7373790	CCDC36	cis	Esophagus Muscularis	GTEx
rs7373790	WDR6	cis	Adipose Subcutaneous	GTEx
rs7373790	NICN1-AS1	cis	Thyroid	GTEx
rs7373790	AMT	cis	Whole Blood	GTEx

Chromatin state (count:127 , 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	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
8	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
9	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
10	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:49067600-49095800	Strong transcription	Dnd41	blood
13	chr3:49067600-49097000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
15	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:49070800-49117000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:49072400-49094200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49073400-49118200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:49074200-49096000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr3:49077400-49117200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:49078800-49091200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:49082600-49091800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:49084400-49094000	Weak transcription	Psoas Muscle	Psoas
25	chr3:49084600-49091000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:49084600-49091000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:49084600-49091200	Weak transcription	Fetal Kidney	kidney
28	chr3:49084600-49091400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:49084600-49093800	Weak transcription	Stomach Mucosa	stomach
30	chr3:49084600-49094000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:49084600-49094000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:49084600-49110800	Weak transcription	Fetal Heart	heart
33	chr3:49084600-49117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:49084800-49094200	Weak transcription	Small Intestine	intestine
35	chr3:49085200-49094000	Weak transcription	Esophagus	oesophagus
36	chr3:49085600-49093800	Weak transcription	A549	lung
37	chr3:49086600-49094200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:49087200-49095800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:49087800-49093000	Strong transcription	Hela-S3	cervix
40	chr3:49087800-49096400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:49087800-49115200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:49087800-49117600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:49088000-49091200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:49088000-49091800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:49088000-49095400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:49088000-49095400	Strong transcription	Fetal Brain Female	brain
47	chr3:49088000-49095400	Strong transcription	Osteobl	bone
48	chr3:49088000-49095600	Strong transcription	Brain Germinal Matrix	brain
49	chr3:49088000-49095600	Strong transcription	Brain Hippocampus Middle	brain
50	chr3:49088000-49095600	Strong transcription	Brain Inferior Temporal Lobe	brain

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