Variant report

Variant	rs2629751
Chromosome Location	chr12:104421808-104421809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12427086	0.92[ASN][1000 genomes]
rs12581921	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1564892	0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs17035129	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17035153	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2583230	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2629798	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs2722170	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2722175	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2723867	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55675238	0.98[ASN][1000 genomes]
rs55997300	0.98[ASN][1000 genomes]
rs56269347	0.84[ASN][1000 genomes]
rs57041861	0.88[ASN][1000 genomes]
rs7358625	0.88[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hepatitis C induced liver fibrosis	22841784	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2629751	CHST11	cis	parietal	SCAN
rs2629751	GLT8D2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104408800-104428000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:104408800-104442200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:104415200-104435200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:104420000-104435200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:104421000-104422200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr12:104421200-104422000	Enhancers	Ovary	ovary
7	chr12:104421200-104435200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:104421600-104422000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:104421600-104422000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:104421800-104422200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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

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