Variant report

Variant	rs12485678
Chromosome Location	chr3:42767868-42767869
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12486439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487055	0.80[CEU][hapmap];0.97[EUR][1000 genomes]
rs12488174	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490743	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492886	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493321	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495805	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061576	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs13064320	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072026	0.81[CEU][hapmap];0.97[EUR][1000 genomes]
rs13085272	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090185	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095730	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1871121	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2240860	0.81[CEU][hapmap];0.97[EUR][1000 genomes]
rs2290972	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2372111	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2372114	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339693	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs339695	0.86[ASN][1000 genomes]
rs339696	0.86[ASN][1000 genomes]
rs34025253	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34188562	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34336220	0.85[AMR][1000 genomes]
rs34482203	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34510173	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34648075	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34974363	0.85[AMR][1000 genomes]
rs35389123	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35488977	0.85[AMR][1000 genomes]
rs35647815	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35659560	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35697625	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35766391	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36061398	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912102	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3912103	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916333	0.96[EUR][1000 genomes]
rs4488806	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]
rs55799024	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56232384	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56978598	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246607	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246631	0.85[AMR][1000 genomes]
rs62250122	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66665035	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6765740	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779396	0.97[EUR][1000 genomes]
rs6799524	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7429327	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7617368	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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
rs12485678	CCDC13	cis	Thyroid	GTEx
rs12485678	CCDC13-AS1	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42760400-42769600	Weak transcription	Right Atrium	heart
2	chr3:42760400-42773600	Enhancers	Brain Substantia Nigra	brain
3	chr3:42761200-42768600	Weak transcription	Left Ventricle	heart
4	chr3:42762800-42768000	Enhancers	Brain Hippocampus Middle	brain
5	chr3:42763600-42773600	Enhancers	Brain Anterior Caudate	brain
6	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
7	chr3:42763800-42771400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:42764000-42771000	Weak transcription	Psoas Muscle	Psoas
9	chr3:42764800-42768000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:42765000-42769000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42765000-42771000	Weak transcription	Right Ventricle	heart
12	chr3:42765000-42772600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:42765200-42770800	Weak transcription	Fetal Heart	heart
14	chr3:42766000-42768600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:42766400-42768000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:42766600-42768000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:42767600-42772600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:42767800-42774400	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links