Variant report

Variant	rs13020054
Chromosome Location	chr2:12078710-12078711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10197022	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11891008	0.82[AMR][1000 genomes]
rs12692449	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12992621	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13003710	1.00[YRI][hapmap]
rs13004740	0.84[EUR][1000 genomes]
rs13011455	0.80[AMR][1000 genomes]
rs13016049	0.86[AMR][1000 genomes]
rs13020034	0.82[AMR][1000 genomes]
rs13025593	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13034603	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2033873	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4669790	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4669792	0.83[AMR][1000 genomes]
rs9287740	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9287741	0.88[AMR][1000 genomes];0.83[EUR][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	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv833403	chr2:11944552-12125634	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13020054	KCNF1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12071200-12081200	Weak transcription	Right Atrium	heart
2	chr2:12072600-12084600	Weak transcription	Primary B cells from cord blood	blood
3	chr2:12074400-12084200	Weak transcription	GM12878-XiMat	blood
4	chr2:12078000-12078800	Enhancers	Fetal Muscle Leg	muscle
5	chr2:12078000-12079400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:12078000-12079400	Enhancers	HMEC	breast
7	chr2:12078000-12080200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:12078200-12078800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:12078200-12078800	Enhancers	Fetal Stomach	stomach
10	chr2:12078200-12078800	Enhancers	HSMM	muscle
11	chr2:12078200-12079000	Flanking Active TSS	NHEK	skin
12	chr2:12078200-12079400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:12078400-12078800	Enhancers	HSMMtube	muscle
14	chr2:12078600-12079200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:12078600-12079200	Weak transcription	Esophagus	oesophagus

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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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