Variant report

Variant	rs11168411
Chromosome Location	chr12:48505003-48505004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10875716	1.00[LWK][hapmap];0.81[MKK][hapmap]
rs11168338	0.83[LWK][hapmap]
rs11168437	1.00[LWK][hapmap]
rs1476607	1.00[LWK][hapmap]
rs7971880	0.81[MKK][hapmap]
rs7975632	1.00[LWK][hapmap]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11168411	PRKAG1	cis	parietal	SCAN
rs11168411	SNORA2A	cis	cerebellum	SCAN
rs11168411	PFKM	cis	parietal	SCAN
rs11168411	RPAP3	cis	cerebellum	SCAN
rs11168411	DBX2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48501000-48508800	Weak transcription	K562	blood
2	chr12:48501200-48512200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:48501600-48506600	Weak transcription	Fetal Intestine Small	intestine
4	chr12:48503800-48505200	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr12:48503800-48505200	Enhancers	Hela-S3	cervix
6	chr12:48504800-48506200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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