Variant report

Variant	rs55713230
Chromosome Location	chr3:49198091-49198092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49197673..49199686-chr3:49449232..49451070,2	K562	blood:
2	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
3	chr3:49166454..49167956-chr3:49197730..49200400,2	K562	blood:
4	chr3:49057940..49060006-chr3:49197956..49200673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000067560	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10154895	0.97[ASN][1000 genomes]
rs10865954	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130182	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130184	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130185	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11552724	0.87[ASN][1000 genomes]
rs11706189	0.97[ASN][1000 genomes]
rs11712006	0.87[ASN][1000 genomes]
rs11713297	0.97[ASN][1000 genomes]
rs11715581	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716334	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717524	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11719220	0.81[ASN][1000 genomes]
rs11920267	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12487580	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490393	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493001	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629637	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12629759	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12631989	0.91[EUR][1000 genomes]
rs12636030	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637576	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064780	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13064784	0.82[ASN][1000 genomes]
rs13096406	0.89[ASN][1000 genomes]
rs2117938	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2334958	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3212	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34326553	0.87[ASN][1000 genomes]
rs34580506	0.87[ASN][1000 genomes]
rs34889065	0.87[ASN][1000 genomes]
rs35174559	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35218722	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35283189	0.87[ASN][1000 genomes]
rs35673421	0.87[ASN][1000 genomes]
rs4279134	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4308307	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4364202	0.80[ASN][1000 genomes]
rs4367098	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4499638	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513485	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4521268	0.82[ASN][1000 genomes]
rs4536858	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955410	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955418	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955419	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955420	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955432	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5030795	0.87[ASN][1000 genomes]
rs61583136	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62262517	0.80[ASN][1000 genomes]
rs66991555	0.87[ASN][1000 genomes]
rs6770112	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6779394	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784111	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790914	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794924	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795756	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7626445	0.82[ASN][1000 genomes]
rs7638154	0.81[EUR][1000 genomes]
rs7645551	0.82[EUR][1000 genomes]
rs7652746	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9814987	0.92[ASN][1000 genomes]
rs9835439	0.92[ASN][1000 genomes]
rs9837237	0.95[ASN][1000 genomes]
rs9837625	0.95[ASN][1000 genomes]
rs9840050	0.82[ASN][1000 genomes]
rs9855123	0.92[ASN][1000 genomes]
rs9862483	0.97[ASN][1000 genomes]
rs9880088	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv3490861	chr3:49196144-49198530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3403660	chr3:49197548-49198596	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	esv8967	chr3:49197550-49198293	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv2063886	chr3:49197581-49198251	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv3461839	chr3:49197634-49198167	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	esv3490862	chr3:49197638-49198185	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv3490860	chr3:49197677-49198109	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv3428996	chr3:49197677-49198192	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	esv3461837	chr3:49197693-49198141	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	esv3712	chr3:49197694-49198254	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	esv3447982	chr3:49197695-49198126	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	esv3461838	chr3:49197697-49198100	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	esv3490864	chr3:49197704-49198167	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	esv3393606	chr3:49197715-49198096	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs55713230	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs55713230	AMT	cis	Artery Aorta	GTEx
rs55713230	CCDC36	cis	Artery Tibial	GTEx
rs55713230	WDR6	cis	Muscle Skeletal	GTEx
rs55713230	WDR6	cis	Nerve Tibial	GTEx
rs55713230	WDR6	cis	lung	GTEx
rs55713230	WDR6	cis	Esophagus Mucosa	GTEx
rs55713230	WDR6	cis	Heart Left Ventricle	GTEx
rs55713230	NCKIPSD	cis	Muscle Skeletal	GTEx
rs55713230	AMT	cis	Muscle Skeletal	GTEx
rs55713230	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs55713230	NICN1	cis	Thyroid	GTEx
rs55713230	ARIH2	cis	Thyroid	GTEx
rs55713230	NCKIPSD	cis	Esophagus Mucosa	GTEx
rs55713230	WDR6	cis	Artery Tibial	GTEx
rs55713230	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs55713230	WDR6	cis	Whole Blood	GTEx
rs55713230	WDR6	cis	Adipose Subcutaneous	GTEx
rs55713230	WDR6	cis	Esophagus Muscularis	GTEx
rs55713230	CCDC36	cis	Esophagus Muscularis	GTEx
rs55713230	NICN1-AS1	cis	Thyroid	GTEx
rs55713230	AMT	cis	Thyroid	GTEx
rs55713230	AMT	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49186200-49198800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:49186800-49198800	Weak transcription	Pancreas	Pancrea
4	chr3:49191000-49198800	Weak transcription	Ovary	ovary
5	chr3:49191000-49199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49191400-49198800	Weak transcription	Gastric	stomach
7	chr3:49191400-49199000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:49191600-49200200	Weak transcription	Esophagus	oesophagus
9	chr3:49192200-49198600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:49194400-49198200	Weak transcription	Brain Germinal Matrix	brain
11	chr3:49194400-49199000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:49194600-49198200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:49194600-49198800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:49194800-49198200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:49195000-49198200	Weak transcription	Fetal Brain Female	brain
16	chr3:49195000-49198200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:49195000-49199600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:49195200-49199400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:49195200-49200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:49195200-49202400	Weak transcription	Fetal Kidney	kidney
21	chr3:49195400-49198800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:49195400-49200400	Weak transcription	Brain Angular Gyrus	brain
23	chr3:49195600-49198200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:49195600-49198200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:49195600-49198600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:49195600-49198600	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:49195600-49198800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:49195600-49198800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:49195600-49198800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:49195600-49199000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:49195600-49199400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:49195600-49199400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:49195600-49200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:49195600-49200200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:49195600-49200400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:49195600-49200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:49195600-49200400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:49195600-49200400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:49195600-49202200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:49195800-49198200	Weak transcription	Brain Substantia Nigra	brain
41	chr3:49195800-49198800	Weak transcription	Fetal Intestine Large	intestine
42	chr3:49195800-49199600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:49196000-49198200	Weak transcription	Fetal Thymus	thymus
44	chr3:49196000-49202400	Strong transcription	Fetal Stomach	stomach
45	chr3:49196200-49200200	Weak transcription	Fetal Lung	lung
46	chr3:49196400-49198800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:49196400-49199200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:49196400-49200400	Weak transcription	HepG2	liver
49	chr3:49196400-49202200	Weak transcription	Right Atrium	heart
50	chr3:49196600-49198200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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