Variant report

Variant	rs339681
Chromosome Location	chr3:42797731-42797732
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42796140..42798050-chr3:42801368..42804341,2	K562	blood:
2	chr3:42791198..42793006-chr3:42796472..42798021,2	K562	blood:
3	chr3:42796446..42798021-chr3:42824548..42826746,2	K562	blood:
4	chr3:42588616..42589577-chr3:42797036..42797865,3	K562	blood:
5	chr3:42592301..42594170-chr3:42795995..42797942,2	K562	blood:

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

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

rs_ID	r²[population]
rs11079	0.85[JPT][hapmap]
rs11717346	0.89[YRI][hapmap]
rs12487055	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12488174	0.97[EUR][1000 genomes]
rs12490743	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12492886	0.82[CEU][hapmap]
rs12493321	0.80[EUR][1000 genomes]
rs12495805	0.82[CEU][hapmap]
rs13061576	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs13064320	0.97[EUR][1000 genomes]
rs13072026	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13085272	0.82[CEU][hapmap]
rs13090185	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs13095730	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17317763	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs1871121	0.95[EUR][1000 genomes]
rs2240860	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290973	0.85[JPT][hapmap]
rs2372111	0.97[EUR][1000 genomes]
rs339664	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs339668	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs339676	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs339694	0.83[JPT][hapmap]
rs339697	0.85[JPT][hapmap]
rs34025253	0.81[EUR][1000 genomes]
rs34336220	0.88[EUR][1000 genomes]
rs34510173	0.81[EUR][1000 genomes]
rs34648075	0.94[EUR][1000 genomes]
rs34974363	0.88[EUR][1000 genomes]
rs35488977	0.88[EUR][1000 genomes]
rs35647815	0.95[EUR][1000 genomes]
rs35659560	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35697625	0.80[EUR][1000 genomes]
rs35766391	0.97[EUR][1000 genomes]
rs35919797	0.87[EUR][1000 genomes]
rs36061398	0.80[EUR][1000 genomes]
rs3846062	0.85[JPT][hapmap]
rs3912102	0.83[CEU][hapmap]
rs3916333	0.82[ASN][1000 genomes]
rs4488806	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs62246607	0.81[EUR][1000 genomes]
rs62246631	0.88[EUR][1000 genomes]
rs62246641	0.86[EUR][1000 genomes]
rs6764909	0.89[YRI][hapmap]
rs6765740	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs6779396	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6799524	0.88[EUR][1000 genomes]
rs7429327	0.95[EUR][1000 genomes]
rs7617368	0.82[CEU][hapmap]

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
rs339681	CCDC13	cis	Thyroid	GTEx
rs339681	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:35 , 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	chr3:42788800-42799800	Weak transcription	Left Ventricle	heart
5	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:42791600-42803000	Weak transcription	Colonic Mucosa	Colon
8	chr3:42791800-42797800	Weak transcription	Pancreas	Pancrea
9	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
10	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:42792000-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:42793600-42802600	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:42793600-42802600	Weak transcription	Brain Substantia Nigra	brain
14	chr3:42793600-42811000	Weak transcription	Lung	lung
15	chr3:42795600-42814000	Weak transcription	Gastric	stomach
16	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
17	chr3:42796000-42799000	Enhancers	Fetal Intestine Large	intestine
18	chr3:42796000-42799000	Enhancers	Fetal Intestine Small	intestine
19	chr3:42796400-42801400	Weak transcription	Placenta	Placenta
20	chr3:42797000-42798400	Enhancers	Adipose Nuclei	Adipose
21	chr3:42797200-42797800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:42797200-42797800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr3:42797200-42798000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:42797200-42798000	Flanking Active TSS	HepG2	liver
25	chr3:42797200-42798200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:42797200-42798200	Enhancers	Brain Anterior Caudate	brain
27	chr3:42797200-42798400	Enhancers	Duodenum Mucosa	Duodenum
28	chr3:42797200-42798600	Enhancers	Liver	Liver
29	chr3:42797200-42798600	Enhancers	Stomach Mucosa	stomach
30	chr3:42797400-42797800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:42797400-42797800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:42797400-42798200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:42797600-42799200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:42797600-42802800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:42797600-42803800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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