Variant report

Variant	rs9990060
Chromosome Location	chr3:46125575-46125576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46123578..46126069-chr3:46127195..46129826,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10510747	1.00[ASN][1000 genomes]
rs1118021	0.92[ASN][1000 genomes]
rs12054287	0.81[CHB][hapmap]
rs12485978	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12486449	0.98[ASN][1000 genomes]
rs13320534	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs13434141	0.98[ASN][1000 genomes]
rs1388602	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1491959	0.80[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs1491960	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs1546077	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs1546079	0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1602580	0.92[ASN][1000 genomes]
rs1604068	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17078567	0.93[ASN][1000 genomes]
rs17078589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036295	0.89[ASN][1000 genomes]
rs2173639	0.89[ASN][1000 genomes]
rs2888512	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4490402	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.91[ASN][1000 genomes]
rs4586860	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682804	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682805	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682807	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682809	0.80[AFR][1000 genomes]
rs4682810	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs4683169	0.81[ASN][1000 genomes]
rs4683174	0.91[ASN][1000 genomes]
rs60991632	0.81[ASN][1000 genomes]
rs61066315	0.95[ASN][1000 genomes]
rs61079448	0.80[AFR][1000 genomes]
rs61387489	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62242846	0.89[ASN][1000 genomes]
rs62243869	0.91[ASN][1000 genomes]
rs62243873	1.00[ASN][1000 genomes]
rs62243875	0.84[ASN][1000 genomes]
rs62243876	0.84[ASN][1000 genomes]
rs6778958	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795629	0.81[JPT][hapmap];0.80[AFR][1000 genomes]
rs6807854	0.81[ASN][1000 genomes]
rs751625	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7623476	0.86[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs7641151	0.97[ASN][1000 genomes]
rs7641164	0.97[ASN][1000 genomes]
rs880160	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818635	0.88[ASN][1000 genomes]
rs9849715	0.97[ASN][1000 genomes]
rs9856805	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9990060	CCDC12	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46120600-46127200	Weak transcription	Fetal Stomach	stomach
2	chr3:46120800-46127000	Weak transcription	HSMMtube	muscle
3	chr3:46120800-46129400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:46121400-46126800	Weak transcription	Fetal Thymus	thymus
5	chr3:46121600-46125800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:46121800-46126000	Enhancers	NHEK	skin
7	chr3:46122600-46127000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:46122800-46126600	Weak transcription	Ovary	ovary
9	chr3:46123000-46127600	Weak transcription	Hela-S3	cervix
10	chr3:46123200-46125800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:46123200-46125800	Enhancers	HMEC	breast
12	chr3:46123200-46126200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr3:46123200-46127000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:46123200-46129600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:46123400-46125800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:46123400-46130400	Weak transcription	Adipose Nuclei	Adipose
17	chr3:46123600-46125800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:46123800-46125600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:46124600-46127000	Weak transcription	Fetal Lung	lung
20	chr3:46125000-46127200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:46125200-46127400	Weak transcription	Placenta	Placenta
22	chr3:46125400-46127800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:46125400-46128400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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