Variant report

Variant	rs62246607
Chromosome Location	chr3:42792986-42792987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42792752..42794704-chr3:42802207..42805435,3	K562	blood:
2	chr3:42694253..42696988-chr3:42790179..42793098,2	K562	blood:
3	chr3:42791485..42794252-chr3:42803648..42805435,2	K562	blood:
4	chr3:42791198..42793006-chr3:42796472..42798021,2	K562	blood:
5	chr3:42787545..42791354-chr3:42791558..42794985,4	K562	blood:

Variant related genes	Relation type
ENSG00000114853	Chromatin interaction
ENSG00000230084	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12485678	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486439	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487055	0.94[EUR][1000 genomes]
rs12488174	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490743	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492886	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493321	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495805	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061576	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13064320	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072026	0.95[EUR][1000 genomes]
rs13085272	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13090185	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095730	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871121	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240860	0.95[EUR][1000 genomes]
rs2372111	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2372114	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339681	0.81[EUR][1000 genomes]
rs339693	0.83[ASN][1000 genomes]
rs339695	0.83[ASN][1000 genomes]
rs339696	0.83[ASN][1000 genomes]
rs34025253	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34188562	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34336220	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34482203	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34648075	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34974363	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35389123	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35488977	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35647815	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35659560	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35697625	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35766391	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36061398	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3912102	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912103	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3916333	0.93[EUR][1000 genomes]
rs4488806	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55799024	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56232384	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56978598	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246602	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246631	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62250122	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66665035	0.86[ASN][1000 genomes]
rs6765740	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779396	0.95[EUR][1000 genomes]
rs6799524	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7429327	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617368	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62246607	CCDC13	cis	Thyroid	GTEx
rs62246607	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:42788200-42794400	Weak transcription	Stomach Mucosa	stomach
4	chr3:42788400-42797200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:42788600-42793400	Weak transcription	Fetal Brain Male	brain
6	chr3:42788600-42796000	Weak transcription	Adipose Nuclei	Adipose
7	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:42788800-42793000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:42788800-42794400	Weak transcription	Gastric	stomach
10	chr3:42788800-42799800	Weak transcription	Left Ventricle	heart
11	chr3:42789000-42795200	Weak transcription	Aorta	Aorta
12	chr3:42789000-42795600	Weak transcription	Fetal Brain Female	brain
13	chr3:42789400-42793000	Weak transcription	Lung	lung
14	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:42790200-42793200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:42790600-42793600	Enhancers	Placenta	Placenta
17	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
18	chr3:42791400-42795400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:42791400-42797200	Weak transcription	Fetal Heart	heart
20	chr3:42791600-42797400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:42791600-42803000	Weak transcription	Colonic Mucosa	Colon
22	chr3:42791800-42793000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:42791800-42793000	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:42791800-42793000	Weak transcription	Fetal Stomach	stomach
25	chr3:42791800-42797000	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:42791800-42797200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:42791800-42797200	Weak transcription	Brain Anterior Caudate	brain
28	chr3:42791800-42797800	Weak transcription	Pancreas	Pancrea
29	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
30	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:42792000-42793000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:42792000-42793000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:42792000-42793000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:42792000-42793000	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:42792000-42793000	Weak transcription	Brain Substantia Nigra	brain
36	chr3:42792000-42793000	Weak transcription	Right Atrium	heart
37	chr3:42792000-42793200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:42792000-42795600	Weak transcription	HepG2	liver
39	chr3:42792000-42797200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:42792000-42797200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:42792000-42797200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr3:42792000-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:42792600-42793400	Enhancers	Fetal Lung	lung
44	chr3:42792600-42793400	Enhancers	Stomach Smooth Muscle	stomach
45	chr3:42792800-42793400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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