Variant report

Variant	rs2372111
Chromosome Location	chr3:42801920-42801921
allele	G/T
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	YY1	chr3:42801864-42802206	HepG2	liver:	n/a	n/a
2	FOS	chr3:42801896-42802676	MCF10A-Er-Src	breast:	n/a	n/a
3	BCL3	chr3:42801892-42802225	GM12878	blood:	n/a	n/a
4	CEBPB	chr3:42801878-42802299	A549	lung:	n/a	chr3:42802151-42802162 chr3:42802197-42802208
5	CEBPB	chr3:42801897-42802526	Hela-S3	cervix:	n/a	chr3:42802151-42802162 chr3:42802197-42802208
6	CEBPB	chr3:42801825-42802388	HCT-116	colon:	n/a	chr3:42802151-42802162 chr3:42802197-42802208
7	TCF3	chr3:42801912-42802245	GM12878	blood:	n/a	n/a
8	FOS	chr3:42801896-42802586	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:42801897-42802312	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42796140..42798050-chr3:42801368..42804341,2	K562	blood:

Variant related genes	Relation type
CCDC13	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12485678	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486439	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488174	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490743	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492886	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493321	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495805	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13061576	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064320	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085272	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13090185	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095730	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17317763	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1871121	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2372114	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs339681	0.97[EUR][1000 genomes]
rs339693	0.83[ASN][1000 genomes]
rs339695	0.83[ASN][1000 genomes]
rs339696	0.83[ASN][1000 genomes]
rs34025253	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34188562	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34336220	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34482203	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34510173	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34648075	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34974363	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35389123	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35488977	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35647815	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35697625	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35766391	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35919797	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36061398	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912102	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3912103	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4488806	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799024	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56232384	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56978598	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246602	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246607	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246631	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62246641	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62250122	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66665035	0.83[ASN][1000 genomes]
rs6765740	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799524	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7429327	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617368	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2372111	CCDC13	cis	Thyroid	GTEx
rs2372111	CCDC13-AS1	cis	Thyroid	GTEx
rs2372111	CCDC13-AS1	cis	Whole Blood	GTEx

Chromatin state (count:31 , 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	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:42791600-42803000	Weak transcription	Colonic Mucosa	Colon
7	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
8	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:42792000-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:42793600-42802600	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:42793600-42802600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:42793600-42811000	Weak transcription	Lung	lung
13	chr3:42795600-42814000	Weak transcription	Gastric	stomach
14	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
15	chr3:42797600-42802800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:42797600-42803800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:42798200-42802600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:42798400-42802400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:42798600-42802400	Weak transcription	Liver	Liver
20	chr3:42798600-42804000	Weak transcription	Stomach Mucosa	stomach
21	chr3:42798800-42803800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:42799000-42803400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:42799200-42802400	Weak transcription	HepG2	liver
24	chr3:42800400-42808600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:42801400-42802000	Enhancers	Placenta	Placenta
26	chr3:42801400-42802400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:42801400-42803400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:42801800-42802200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:42801800-42802200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:42801800-42802600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:42801800-42802800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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