Variant report

Variant	rs4488806
Chromosome Location	chr3:42804608-42804609
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: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12485678	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];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]
rs12487055	0.81[CEU][hapmap]
rs12488174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490743	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492886	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];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	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13061576	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072026	0.81[CEU][hapmap]
rs13085272	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13090185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095730	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17317763	1.00[CEU][hapmap];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]
rs2240860	0.81[CEU][hapmap]
rs2290972	0.80[CHB][hapmap];1.00[JPT][hapmap]
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	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs339693	1.00[JPT][hapmap];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	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];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]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];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
rs4488806	CCDC13-AS1	cis	Thyroid	GTEx
rs4488806	CCDC13	cis	Thyroid	GTEx

Chromatin state (count:41 , 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	chr3:42802400-42804800	Enhancers	Adipose Nuclei	Adipose
10	chr3:42802400-42804800	Enhancers	NHDF-Ad	bronchial
11	chr3:42802400-42805000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:42802400-42805000	Enhancers	HepG2	liver
13	chr3:42802400-42806400	Enhancers	Placenta	Placenta
14	chr3:42802600-42805000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:42802600-42805000	Enhancers	Brain Anterior Caudate	brain
16	chr3:42802600-42805000	Enhancers	Osteobl	bone
17	chr3:42802600-42805400	Enhancers	Brain Cingulate Gyrus	brain
18	chr3:42802600-42806200	Enhancers	Brain Substantia Nigra	brain
19	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
20	chr3:42803200-42806000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:42803400-42804800	Enhancers	Fetal Intestine Small	intestine
22	chr3:42803400-42805000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:42803400-42805800	Weak transcription	Colonic Mucosa	Colon
24	chr3:42803400-42806000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:42803400-42806400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:42803600-42805000	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:42803800-42805400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr3:42804000-42804800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:42804000-42804800	Enhancers	Colon Smooth Muscle	Colon
30	chr3:42804000-42804800	Enhancers	Fetal Stomach	stomach
31	chr3:42804200-42804800	Enhancers	Fetal Heart	heart
32	chr3:42804200-42804800	Enhancers	GM12878-XiMat	blood
33	chr3:42804200-42805000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr3:42804200-42814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:42804400-42805800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:42804400-42807400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:42804600-42804800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:42804600-42804800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:42804600-42804800	Enhancers	A549	lung
40	chr3:42804600-42805800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr3:42804600-42806000	Weak transcription	Primary B cells from cord blood	blood

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