Variant report

Variant	rs28661038
Chromosome Location	chr5:68750184-68750185
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10067619	0.82[ASN][1000 genomes]
rs12519819	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12519823	0.87[EUR][1000 genomes]
rs28429739	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28520694	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28547925	0.89[AMR][1000 genomes]
rs28551092	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28567918	0.83[EUR][1000 genomes]
rs28579732	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28615983	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28661038	OCLN	cis	Thyroid	GTEx
rs28661038	GUSBP3	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68732600-68750400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:68745200-68750200	Enhancers	Stomach Mucosa	stomach
3	chr5:68746800-68750400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:68748600-68750400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:68748800-68751000	Enhancers	Pancreas	Pancrea
6	chr5:68749200-68750200	Active TSS	A549	lung
7	chr5:68749600-68750200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr5:68749600-68750400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:68749800-68750600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr5:68750000-68750200	Active TSS	HepG2	liver
11	chr5:68750000-68750400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr5:68750000-68750400	Flanking Active TSS	Fetal Intestine Small	intestine
13	chr5:68750000-68750600	Active TSS	Fetal Intestine Large	intestine
14	chr5:68750000-68750600	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr5:68750000-68751000	Flanking Active TSS	Liver	Liver
16	chr5:68750000-68751000	Active TSS	Duodenum Mucosa	Duodenum
17	chr5:68750000-68751000	Enhancers	Placenta	Placenta

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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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