Variant report

Variant	rs28407209
Chromosome Location	chr5:68786844-68786845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000152939	Chromatin interaction
ENSG00000197822	Chromatin interaction
ENSG00000212260	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10067619	0.85[ASN][1000 genomes]
rs28404493	0.87[AMR][1000 genomes]
rs28429739	0.86[ASN][1000 genomes]
rs28489109	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28513225	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28531719	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28558979	0.87[AMR][1000 genomes]
rs28562181	0.87[AMR][1000 genomes]
rs28579732	0.88[ASN][1000 genomes]
rs28612873	0.87[AMR][1000 genomes]
rs3733742	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806856	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846487	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923832	0.87[AMR][1000 genomes]

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	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1023116	chr5:68744307-68867282	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1034024	chr5:68760271-69118123	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28407209	GUSBP3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68781200-68787600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:68782600-68787600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:68784200-68787800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:68784600-68787400	Enhancers	Fetal Intestine Small	intestine
5	chr5:68785400-68787400	Enhancers	HepG2	liver
6	chr5:68785400-68787800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:68785400-68787800	Weak transcription	Pancreas	Pancrea
8	chr5:68785400-68788000	Weak transcription	Gastric	stomach
9	chr5:68785600-68787200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:68785600-68787400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:68785600-68787800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr5:68786400-68787400	Enhancers	Fetal Intestine Large	intestine
13	chr5:68786600-68787600	Enhancers	Stomach Mucosa	stomach
14	chr5:68786800-68787600	Enhancers	A549	lung
15	chr5:68786800-68788200	Flanking Active TSS	Liver	Liver

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