Variant report

Variant	rs13064320
Chromosome Location	chr3:42812019-42812020
allele	C/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	POLR2A	chr3:42811967-42812244	HepG2	liver:	n/a	n/a
2	MAFF	chr3:42811757-42812118	HepG2	liver:	n/a	chr3:42811930-42811948
3	POLR2A	chr3:42811992-42812185	HepG2	liver:	n/a	n/a
4	HEY1	chr3:42811983-42812257	HepG2	liver:	n/a	n/a
5	NFYB	chr3:42811607-42812147	GM12878	blood:	n/a	chr3:42812020-42812035 chr3:42811972-42811987 chr3:42811996-42812011
6	NFYB	chr3:42811879-42812149	K562	blood:	n/a	chr3:42812020-42812035 chr3:42811972-42811987 chr3:42811996-42812011
7	NFYB	chr3:42811924-42812120	Hela-S3	cervix:	n/a	chr3:42812020-42812035 chr3:42811972-42811987 chr3:42811996-42812011
8	POLR2A	chr3:42811945-42812316	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:42811939-42812170	HepG2	liver:	n/a	n/a
10	MAFK	chr3:42811754-42812117	HepG2	liver:	n/a	chr3:42811953-42811968 chr3:42811931-42811946
11	MAFK	chr3:42811768-42812118	IMR90	lung:	n/a	chr3:42811953-42811968 chr3:42811931-42811946
12	HEY1	chr3:42811978-42812281	HepG2	liver:	n/a	n/a
13	MAFK	chr3:42811881-42812116	HepG2	liver:	n/a	chr3:42811953-42811968 chr3:42811931-42811946
14	TBP	chr3:42811945-42812125	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000225611	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12485678	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486439	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490743	0.85[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	0.85[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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13085272	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13090185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095730	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17317763	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1871121	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2372111	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372114	0.81[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	0.85[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34482203	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34510173	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34648075	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34974363	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35389123	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35488977	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35647815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35697625	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35766391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35919797	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36061398	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912102	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3912103	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4488806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799024	0.85[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	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246602	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246607	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246631	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62246641	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62250122	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66665035	0.83[ASN][1000 genomes]
rs6765740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7429327	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617368	0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13064320	CCDC13	cis	Thyroid	GTEx
rs13064320	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42795600-42814000	Weak transcription	Gastric	stomach
2	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
3	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
4	chr3:42804200-42814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:42805000-42813800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:42807400-42813400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:42807400-42814000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:42808000-42812400	Weak transcription	HepG2	liver
9	chr3:42808000-42814000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:42808000-42814200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:42808800-42813200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:42811200-42814000	Weak transcription	Spleen	Spleen
13	chr3:42811600-42814200	Weak transcription	Lung	lung

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