Variant report

Variant	rs7639332
Chromosome Location	chr3:48934102-48934103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48924606..48926338-chr3:48931670..48934413,2	K562	blood:
2	chr3:48933374..48937590-chr3:48954193..48958596,7	K562	blood:
3	chr3:48928069..48930846-chr3:48933340..48936058,2	K562	blood:
4	chr3:48919442..48921125-chr3:48933903..48935990,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221883	Chromatin interaction
ENSG00000177479	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10780033	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130176	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134591	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11705737	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11705888	0.88[EUR][1000 genomes]
rs11706052	0.82[ASN][1000 genomes]
rs11708022	0.89[ASN][1000 genomes]
rs11709246	0.90[ASN][1000 genomes]
rs11712982	0.97[ASN][1000 genomes]
rs11713694	0.92[ASN][1000 genomes]
rs11717978	1.00[ASN][1000 genomes]
rs11719457	1.00[ASN][1000 genomes]
rs11920534	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11924597	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12491743	0.82[EUR][1000 genomes]
rs12493289	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12637037	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13064883	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064911	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072554	0.82[ASN][1000 genomes]
rs13072911	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13073997	0.95[ASN][1000 genomes]
rs13076394	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13078308	0.92[EUR][1000 genomes]
rs13080725	0.82[ASN][1000 genomes]
rs13086240	0.97[ASN][1000 genomes]
rs13087930	1.00[ASN][1000 genomes]
rs13090839	0.97[ASN][1000 genomes]
rs13094900	0.92[ASN][1000 genomes]
rs13315711	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13316620	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28642807	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34477108	1.00[ASN][1000 genomes]
rs34504524	0.92[ASN][1000 genomes]
rs34509487	1.00[ASN][1000 genomes]
rs35108630	0.82[ASN][1000 genomes]
rs3774628	0.86[EUR][1000 genomes]
rs3923475	0.82[ASN][1000 genomes]
rs4072859	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974078	0.88[ASN][1000 genomes]
rs4974079	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974080	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974082	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974084	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974085	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974087	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974091	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55674449	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56318350	1.00[ASN][1000 genomes]
rs6414613	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6442130	0.84[EUR][1000 genomes]
rs6446196	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446198	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6446205	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446252	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446253	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67060340	0.95[ASN][1000 genomes]
rs67332931	0.90[ASN][1000 genomes]
rs6768433	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6781790	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6786665	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6789285	0.90[EUR][1000 genomes]
rs6791234	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6791542	0.82[EUR][1000 genomes]
rs6795025	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71324924	0.90[ASN][1000 genomes]
rs7372149	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7373778	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7373790	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7430198	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430501	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431710	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431857	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7432989	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7612459	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7615235	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7615675	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7616815	0.84[EUR][1000 genomes]
rs7621015	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7623023	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626445	0.85[EUR][1000 genomes]
rs7627404	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7628719	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7630742	0.81[EUR][1000 genomes]
rs7636057	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7643368	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647093	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7649458	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7653459	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8926	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311430	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311432	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311433	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311434	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9681717	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9682444	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9754878	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9755490	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830636	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835307	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840050	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9840684	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846123	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9850134	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867373	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876848	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879971	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9884022	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs7639332	WDR6	cis	Muscle Skeletal	GTEx
rs7639332	NCKIPSD	cis	Nerve Tibial	GTEx
rs7639332	NCKIPSD	cis	Whole Blood	GTEx
rs7639332	CCDC36	cis	Esophagus Muscularis	GTEx
rs7639332	WDR6	cis	Esophagus Mucosa	GTEx
rs7639332	WDR6	cis	Whole Blood	GTEx
rs7639332	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7639332	AMT	cis	Muscle Skeletal	GTEx
rs7639332	CCDC36	cis	Artery Tibial	GTEx
rs7639332	WDR6	cis	Heart Left Ventricle	GTEx
rs7639332	WDR6	cis	Adipose Subcutaneous	GTEx
rs7639332	NICN1-AS1	cis	Thyroid	GTEx
rs7639332	WDR6	cis	lung	GTEx
rs7639332	WDR6	cis	Esophagus Muscularis	GTEx
rs7639332	AMT	cis	Whole Blood	GTEx
rs7639332	NCKIPSD	cis	Muscle Skeletal	GTEx
rs7639332	ARIH2	cis	Thyroid	GTEx
rs7639332	WDR6	cis	Nerve Tibial	GTEx
rs7639332	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7639332	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7639332	WDR6	cis	Artery Tibial	GTEx
rs7639332	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7639332	NICN1	cis	Thyroid	GTEx
rs7639332	AMT	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48889600-48935400	Weak transcription	Brain Germinal Matrix	brain
2	chr3:48896400-48934400	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:48896800-48934200	Weak transcription	Stomach Mucosa	stomach
4	chr3:48896800-48935000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:48897000-48934200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:48897000-48934200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:48897200-48934200	Weak transcription	Colonic Mucosa	Colon
8	chr3:48897200-48935000	Weak transcription	NH-A	brain
9	chr3:48897200-48935200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:48897400-48934600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:48900200-48935000	Weak transcription	Esophagus	oesophagus
12	chr3:48902600-48935000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:48916600-48935000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:48917000-48934800	Weak transcription	NHDF-Ad	bronchial
15	chr3:48917600-48934200	Weak transcription	Osteobl	bone
16	chr3:48917600-48934800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:48917800-48934200	Weak transcription	GM12878-XiMat	blood
18	chr3:48919400-48935200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:48919600-48934400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:48920000-48934200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:48920400-48934200	Weak transcription	Fetal Heart	heart
22	chr3:48921600-48935000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:48922600-48934400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:48922600-48935000	Weak transcription	Brain Angular Gyrus	brain
25	chr3:48923000-48935000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:48923400-48934200	Weak transcription	Small Intestine	intestine
27	chr3:48923600-48935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:48924800-48934200	Weak transcription	Ovary	ovary
29	chr3:48924800-48934400	Weak transcription	Placenta	Placenta
30	chr3:48924800-48934800	Weak transcription	Right Atrium	heart
31	chr3:48924800-48935200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:48925000-48935000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:48925200-48934800	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:48925400-48935000	Weak transcription	Aorta	Aorta
35	chr3:48926000-48935400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:48926800-48935000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:48928200-48935400	Weak transcription	Fetal Brain Male	brain
38	chr3:48929200-48934800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:48929400-48934200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:48929400-48934200	Weak transcription	Fetal Thymus	thymus
41	chr3:48929400-48934200	Weak transcription	Left Ventricle	heart
42	chr3:48929400-48934200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:48929400-48935600	Weak transcription	Fetal Stomach	stomach
44	chr3:48929600-48934200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:48929600-48934200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:48929600-48934200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:48929600-48934200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:48929600-48934200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:48929600-48934200	Weak transcription	Gastric	stomach
50	chr3:48929600-48934200	Weak transcription	Pancreas	Pancrea

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