Variant report

Variant	rs6779396
Chromosome Location	chr3:42759790-42759791
allele	A/G
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	chr3:42759686-42759833	K562	blood:	n/a	n/a

Variant related genes	Relation type
CCDC13	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11079	0.87[ASN][1000 genomes]
rs12485678	0.97[EUR][1000 genomes]
rs12486439	0.97[EUR][1000 genomes]
rs12487055	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490743	0.95[EUR][1000 genomes]
rs12492886	0.97[EUR][1000 genomes]
rs12493321	0.96[EUR][1000 genomes]
rs12495805	0.97[EUR][1000 genomes]
rs13072026	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085272	0.97[EUR][1000 genomes]
rs13095730	0.95[EUR][1000 genomes]
rs2240860	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2372114	0.90[EUR][1000 genomes]
rs339681	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs339694	0.85[ASN][1000 genomes]
rs339697	0.86[ASN][1000 genomes]
rs34025253	0.95[EUR][1000 genomes]
rs34188562	0.97[EUR][1000 genomes]
rs34378441	0.86[ASN][1000 genomes]
rs34482203	0.93[EUR][1000 genomes]
rs34510173	0.95[EUR][1000 genomes]
rs35389123	0.97[EUR][1000 genomes]
rs35659560	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35697625	0.96[EUR][1000 genomes]
rs36061398	0.96[EUR][1000 genomes]
rs3846062	0.82[ASN][1000 genomes]
rs3912102	0.97[EUR][1000 genomes]
rs3912103	0.95[EUR][1000 genomes]
rs3916333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799024	0.97[EUR][1000 genomes]
rs56232384	0.97[EUR][1000 genomes]
rs56978598	0.97[EUR][1000 genomes]
rs62246602	0.97[EUR][1000 genomes]
rs62246607	0.95[EUR][1000 genomes]
rs62250122	0.97[EUR][1000 genomes]
rs7617368	0.97[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6779396	CCDC13	cis	Thyroid	GTEx
rs6779396	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42747800-42760200	Weak transcription	Right Atrium	heart
2	chr3:42754400-42760600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:42754800-42760200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:42758400-42762000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:42758600-42759800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr3:42759600-42762200	Enhancers	Monocytes-CD14+_RO01746	blood

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