Variant report

Variant	rs11052292
Chromosome Location	chr12:33058258-33058259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11052290	0.85[ASN][1000 genomes]
rs4244861	0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs4931654	0.85[ASN][1000 genomes]
rs7300700	0.86[ASN][1000 genomes]
rs7954545	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[LWK][hapmap];0.85[ASN][1000 genomes]
rs7966440	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1035900	chr12:33010643-33079667	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541458	chr12:33010643-33079667	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11052292	TMTC1	cis	cerebellum	SCAN
rs11052292	OVCH1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:33056000-33058400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:33056000-33058800	Weak transcription	Stomach Mucosa	stomach
3	chr12:33056000-33059000	Weak transcription	GM12878-XiMat	blood
4	chr12:33056000-33060400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:33056200-33058800	Weak transcription	Liver	Liver
6	chr12:33056200-33058800	Weak transcription	HepG2	liver
7	chr12:33057000-33058800	Weak transcription	Left Ventricle	heart
8	chr12:33057000-33059400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:33057200-33058800	Weak transcription	Hela-S3	cervix
10	chr12:33057800-33058600	Weak transcription	Fetal Intestine Small	intestine
11	chr12:33058000-33058800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:33058000-33061800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:33058000-33063400	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr12:33058200-33059000	Enhancers	Fetal Intestine Large	intestine
15	chr12:33058200-33063600	Enhancers	Duodenum Mucosa	Duodenum

Quick Search:

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

what's new

Quick links