Variant report

Variant	rs6453099
Chromosome Location	chr5:74259550-74259551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10045282	0.92[ASN][1000 genomes]
rs10066902	0.91[ASN][1000 genomes]
rs10078075	0.91[ASN][1000 genomes]
rs10805892	0.91[ASN][1000 genomes]
rs10942726	0.80[AMR][1000 genomes]
rs11748722	0.91[ASN][1000 genomes]
rs4235682	0.91[ASN][1000 genomes]
rs4382144	0.91[ASN][1000 genomes]
rs4392602	0.99[ASN][1000 genomes]
rs4413513	0.91[ASN][1000 genomes]
rs4703642	1.00[ASN][1000 genomes]
rs4704162	0.83[ASN][1000 genomes]
rs6453100	0.90[ASN][1000 genomes]
rs6863602	0.91[ASN][1000 genomes]
rs6867482	0.89[ASN][1000 genomes]
rs6883719	0.91[ASN][1000 genomes]
rs6898812	0.91[ASN][1000 genomes]
rs7736223	1.00[ASN][1000 genomes]
rs9293637	1.00[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	nsv830352	chr5:74189495-74337944	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1018865	chr5:74246293-74494552	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6453099	GCNT4	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74253600-74261400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:74253600-74269200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:74254200-74262600	Weak transcription	Pancreas	Pancrea
4	chr5:74255000-74272600	Weak transcription	Gastric	stomach
5	chr5:74256000-74261800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:74258800-74259600	Enhancers	Fetal Intestine Small	intestine
7	chr5:74258800-74259800	Enhancers	Fetal Intestine Large	intestine
8	chr5:74258800-74259800	Enhancers	Stomach Mucosa	stomach
9	chr5:74259000-74259800	Enhancers	NHEK	skin
10	chr5:74259000-74260000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:74259200-74259800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:74259200-74259800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:74259200-74261600	Enhancers	Pancreatic Islets	Pancreatic Islet

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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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