Variant report

Variant	rs2711702
Chromosome Location	chr12:47417972-47417973
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10785649	0.96[EUR][1000 genomes]
rs10881023	0.96[EUR][1000 genomes]
rs10881025	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183695	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183699	0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs2263492	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2408647	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2522258	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2522263	0.86[EUR][1000 genomes]
rs2522269	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2522275	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711695	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2711698	0.98[ASN][1000 genomes]
rs2711699	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768769	0.95[EUR][1000 genomes]
rs7139072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305283	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978006	0.96[EUR][1000 genomes]
rs7979771	0.96[EUR][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	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2711702	CCNT1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47411000-47418200	Enhancers	NHEK	skin
2	chr12:47413800-47418000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:47413800-47418400	Enhancers	HSMMtube	muscle
4	chr12:47414000-47418400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr12:47414000-47418600	Enhancers	HSMM	muscle
6	chr12:47414000-47418800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:47415200-47418600	Enhancers	HMEC	breast
8	chr12:47415200-47419200	Enhancers	Osteobl	bone
9	chr12:47416400-47418200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:47416600-47419400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:47416600-47422800	Weak transcription	A549	lung
12	chr12:47416800-47418400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:47417200-47418000	Weak transcription	NHLF	lung
14	chr12:47417600-47418400	Enhancers	Liver	Liver
15	chr12:47417800-47418000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:47417800-47418600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:47417800-47418800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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