Variant report

Variant	rs34648075
Chromosome Location	chr3:42804925-42804926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42791485..42794252-chr3:42803648..42805435,2	K562	blood:
2	chr3:42792752..42794704-chr3:42802207..42805435,3	K562	blood:
3	chr3:42804568..42808047-chr3:42844352..42847705,4	K562	blood:

Variant related genes	Relation type
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction

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];0.94[ASN][1000 genomes]
rs12486439	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12488174	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490743	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492886	0.94[ASN][1000 genomes]
rs12493321	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495805	0.94[ASN][1000 genomes]
rs13061576	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064320	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085272	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13090185	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095730	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17317763	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1871121	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2372111	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2372114	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs339681	0.94[EUR][1000 genomes]
rs339693	0.83[ASN][1000 genomes]
rs339695	0.83[ASN][1000 genomes]
rs339696	0.83[ASN][1000 genomes]
rs34025253	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34188562	0.94[ASN][1000 genomes]
rs34336220	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34482203	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34510173	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34974363	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35389123	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35488977	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35647815	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35697625	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35766391	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35919797	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36061398	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912102	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3912103	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4488806	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799024	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56232384	0.94[ASN][1000 genomes]
rs56978598	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62246602	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62246607	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246631	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62246641	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62250122	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs66665035	0.83[ASN][1000 genomes]
rs6765740	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799524	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7429327	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7617368	0.83[AMR][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
rs34648075	CCDC13	cis	Thyroid	GTEx
rs34648075	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:42793600-42811000	Weak transcription	Lung	lung
5	chr3:42795600-42814000	Weak transcription	Gastric	stomach
6	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
7	chr3:42800400-42808600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:42802200-42805000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:42802400-42805000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:42802400-42805000	Enhancers	HepG2	liver
11	chr3:42802400-42806400	Enhancers	Placenta	Placenta
12	chr3:42802600-42805000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:42802600-42805000	Enhancers	Brain Anterior Caudate	brain
14	chr3:42802600-42805000	Enhancers	Osteobl	bone
15	chr3:42802600-42805400	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:42802600-42806200	Enhancers	Brain Substantia Nigra	brain
17	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
18	chr3:42803200-42806000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:42803400-42805000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:42803400-42805800	Weak transcription	Colonic Mucosa	Colon
21	chr3:42803400-42806000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:42803400-42806400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:42803600-42805000	Enhancers	Stomach Smooth Muscle	stomach
24	chr3:42803800-42805400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:42804200-42805000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr3:42804200-42814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:42804400-42805800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:42804400-42807400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:42804600-42805800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr3:42804600-42806000	Weak transcription	Primary B cells from cord blood	blood
31	chr3:42804800-42805000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:42804800-42805800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:42804800-42807400	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links