Variant report

Variant	rs12490743
Chromosome Location	chr3:42788914-42788915
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42787545..42791354-chr3:42791558..42794985,4	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12485678	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]
rs12486439	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487055	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs12488174	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493321	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061576	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13064320	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072026	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs13085272	1.00[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]
rs13090185	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17317763	0.85[CEU][hapmap]
rs1871121	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240860	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs2290972	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2372111	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2372114	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339681	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs339693	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs339695	0.83[ASN][1000 genomes]
rs339696	0.83[ASN][1000 genomes]
rs34025253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34188562	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34336220	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34482203	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34648075	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34974363	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35389123	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35488977	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35647815	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35659560	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35697625	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35766391	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36061398	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3912102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912103	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3916333	0.93[EUR][1000 genomes]
rs4488806	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]
rs55799024	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56232384	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56978598	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246602	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246607	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246631	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62250122	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66665035	0.86[ASN][1000 genomes]
rs6765740	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]
rs6779396	0.95[EUR][1000 genomes]
rs6799524	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7429327	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12490743	CCDC13	cis	Whole Blood	GTEx
rs12490743	CCDC13	cis	Thyroid	GTEx
rs12490743	CCDC13-AS1	cis	Thyroid	GTEx
rs12490743	CCDC13-AS1	cis	Whole Blood	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

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	chr3:42785200-42790200	Enhancers	Brain Anterior Caudate	brain
4	chr3:42785200-42792000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr3:42785200-42792000	Enhancers	Brain Substantia Nigra	brain
6	chr3:42785400-42790200	Enhancers	Brain Hippocampus Middle	brain
7	chr3:42785400-42792000	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:42785600-42790200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:42785600-42791600	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:42785600-42791800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:42785800-42791800	Enhancers	Fetal Muscle Leg	muscle
12	chr3:42786400-42789400	Enhancers	Placenta	Placenta
13	chr3:42786400-42790200	Enhancers	Fetal Stomach	stomach
14	chr3:42786600-42789000	Enhancers	Fetal Lung	lung
15	chr3:42786600-42790000	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr3:42786600-42790400	Enhancers	Brain Angular Gyrus	brain
17	chr3:42787000-42789000	Enhancers	Psoas Muscle	Psoas
18	chr3:42787000-42789200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:42787200-42789000	Enhancers	Fetal Brain Female	brain
20	chr3:42787200-42789000	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr3:42787200-42790000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:42787400-42789000	Enhancers	Aorta	Aorta
23	chr3:42787400-42789400	Enhancers	Lung	lung
24	chr3:42787400-42790000	Enhancers	Esophagus	oesophagus
25	chr3:42787400-42790800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:42787400-42791800	Enhancers	Fetal Muscle Trunk	muscle
27	chr3:42787600-42789000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:42787600-42789000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:42787600-42789800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:42787800-42789000	Enhancers	Fetal Thymus	thymus
31	chr3:42787800-42790000	Enhancers	Pancreas	Pancrea
32	chr3:42787800-42790200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr3:42787800-42790800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:42787800-42791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:42788000-42792000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:42788200-42789000	Weak transcription	Brain Germinal Matrix	brain
37	chr3:42788200-42789200	Enhancers	HepG2	liver
38	chr3:42788200-42790200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:42788200-42790200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:42788200-42790800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:42788200-42791000	Weak transcription	Fetal Heart	heart
42	chr3:42788200-42791800	Enhancers	Colon Smooth Muscle	Colon
43	chr3:42788200-42794400	Weak transcription	Stomach Mucosa	stomach
44	chr3:42788400-42789000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr3:42788400-42789600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:42788400-42789800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:42788400-42797200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:42788600-42789000	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr3:42788600-42790000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:42788600-42790200	Enhancers	Primary monocytes fromperipheralblood	blood

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