Variant report

Variant	rs12637037
Chromosome Location	chr3:49075988-49075989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49075986-49076104	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49073963..49076369-chr3:49168247..49170287,2	K562	blood:

Variant related genes	Relation type
QRICH1	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10780033	0.86[EUR][1000 genomes]
rs11130176	0.84[EUR][1000 genomes]
rs1134591	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11552724	0.80[ASN][1000 genomes]
rs11705737	0.92[EUR][1000 genomes]
rs11706052	0.92[ASN][1000 genomes]
rs11712006	0.80[ASN][1000 genomes]
rs11717978	0.80[ASN][1000 genomes]
rs11719457	0.80[ASN][1000 genomes]
rs11920534	0.90[EUR][1000 genomes]
rs11924597	0.90[EUR][1000 genomes]
rs12491743	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12493289	0.86[EUR][1000 genomes]
rs13064784	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13064883	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13064911	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13072554	0.92[ASN][1000 genomes]
rs13072911	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13076394	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13078308	0.81[EUR][1000 genomes]
rs13080725	0.92[ASN][1000 genomes]
rs13086240	0.82[ASN][1000 genomes]
rs13087930	0.80[ASN][1000 genomes]
rs13315711	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13316620	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28642807	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3212	0.80[EUR][1000 genomes]
rs34326553	0.80[ASN][1000 genomes]
rs34477108	0.80[ASN][1000 genomes]
rs34504524	0.87[ASN][1000 genomes]
rs34509487	0.80[ASN][1000 genomes]
rs34580506	0.80[ASN][1000 genomes]
rs34889065	0.80[ASN][1000 genomes]
rs35108630	0.92[ASN][1000 genomes]
rs35283189	0.80[ASN][1000 genomes]
rs35673421	0.80[ASN][1000 genomes]
rs3923475	0.92[ASN][1000 genomes]
rs4072859	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4279134	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4364202	0.83[ASN][1000 genomes]
rs4974079	0.86[EUR][1000 genomes]
rs4974080	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974082	0.93[EUR][1000 genomes]
rs4974084	0.86[EUR][1000 genomes]
rs4974085	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4974087	0.88[EUR][1000 genomes]
rs4974091	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5030795	0.80[ASN][1000 genomes]
rs56318350	0.80[ASN][1000 genomes]
rs62262517	0.84[EUR][1000 genomes]
rs6414613	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6446196	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446198	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6446205	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6446252	0.86[EUR][1000 genomes]
rs6446253	0.86[EUR][1000 genomes]
rs6768433	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6772452	0.92[AFR][1000 genomes]
rs6779394	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6781790	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6786665	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6789285	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791234	0.91[EUR][1000 genomes]
rs6795025	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7372149	0.86[EUR][1000 genomes]
rs7373778	0.83[EUR][1000 genomes]
rs7373790	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7430198	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7430501	0.86[EUR][1000 genomes]
rs7431710	0.89[EUR][1000 genomes]
rs7431857	0.86[EUR][1000 genomes]
rs7432989	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612459	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615235	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7615675	0.89[EUR][1000 genomes]
rs7621015	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7623023	0.87[EUR][1000 genomes]
rs7626445	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7627404	0.84[EUR][1000 genomes]
rs7628719	0.93[EUR][1000 genomes]
rs7636057	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7639332	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7643368	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7647093	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7649458	0.85[EUR][1000 genomes]
rs8926	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9311430	0.84[EUR][1000 genomes]
rs9311432	0.84[EUR][1000 genomes]
rs9311433	0.84[EUR][1000 genomes]
rs9311434	0.85[EUR][1000 genomes]
rs9681717	0.86[EUR][1000 genomes]
rs9682444	0.84[EUR][1000 genomes]
rs9754878	0.86[EUR][1000 genomes]
rs9755490	0.86[EUR][1000 genomes]
rs9830636	0.82[EUR][1000 genomes]
rs9835307	0.84[EUR][1000 genomes]
rs9840050	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9840684	0.86[EUR][1000 genomes]
rs9841640	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9846123	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850134	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9867373	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9876848	0.84[EUR][1000 genomes]
rs9879971	0.86[EUR][1000 genomes]
rs9884022	0.83[AMR][1000 genomes];0.92[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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs12637037	WDR6	cis	Muscle Skeletal	GTEx
rs12637037	WDR6	cis	Heart Left Ventricle	GTEx
rs12637037	NCKIPSD	cis	Nerve Tibial	GTEx
rs12637037	WDR6	cis	Whole Blood	GTEx
rs12637037	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs12637037	NICN1	cis	Thyroid	GTEx
rs12637037	AMT	cis	Artery Aorta	GTEx
rs12637037	WDR6	cis	Esophagus Muscularis	GTEx
rs12637037	WDR6	cis	lung	GTEx
rs12637037	AMT	cis	Whole Blood	GTEx
rs12637037	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12637037	WDR6	cis	Nerve Tibial	GTEx
rs12637037	WDR6	cis	Artery Tibial	GTEx
rs12637037	NICN1-AS1	cis	Thyroid	GTEx
rs12637037	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs12637037	CCDC36	cis	Artery Tibial	GTEx
rs12637037	AMT	cis	Thyroid	GTEx
rs12637037	NCKIPSD	cis	Whole Blood	GTEx
rs12637037	WDR6	cis	Adipose Subcutaneous	GTEx
rs12637037	WDR6	cis	Esophagus Mucosa	GTEx
rs12637037	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs12637037	NCKIPSD	cis	Muscle Skeletal	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	chr3:49067200-49078600	Weak transcription	Psoas Muscle	Psoas
4	chr3:49067200-49085600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
6	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:49067400-49076400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:49067400-49077200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:49067400-49079800	Strong transcription	Placenta	Placenta
10	chr3:49067400-49085000	Strong transcription	Brain Germinal Matrix	brain
11	chr3:49067400-49085600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:49067400-49085600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:49067400-49085600	Strong transcription	Fetal Intestine Large	intestine
14	chr3:49067400-49086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:49067400-49086600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:49067400-49090000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
20	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
21	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
22	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:49067600-49080200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:49067600-49085600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:49067600-49085600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:49067600-49085600	Strong transcription	Liver	Liver
28	chr3:49067600-49086600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:49067600-49086800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:49067600-49095800	Strong transcription	Dnd41	blood
31	chr3:49067600-49097000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
33	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:49067800-49076000	Strong transcription	Brain Hippocampus Middle	brain
35	chr3:49067800-49076400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:49067800-49086800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:49067800-49086800	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:49068200-49081200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:49070600-49076600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:49070600-49079800	Weak transcription	A549	lung
42	chr3:49070600-49085000	Strong transcription	Adipose Nuclei	Adipose
43	chr3:49070800-49077000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:49070800-49078200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:49070800-49078200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:49070800-49078400	Weak transcription	Colonic Mucosa	Colon
47	chr3:49070800-49079600	Weak transcription	Esophagus	oesophagus
48	chr3:49070800-49083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:49070800-49084600	Strong transcription	Fetal Lung	lung
50	chr3:49070800-49085600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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