Variant report

Variant	rs6552116
Chromosome Location	chr4:68672416-68672417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13114094	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899218	1.00[ASN][1000 genomes]
rs2165363	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs41371952	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6552118	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824984	1.00[ASN][1000 genomes]
rs6831736	0.94[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312189	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv879214	chr4:68389841-68789778	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv829960	chr4:68649237-68809629	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3446954	chr4:68653705-68709553	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6552116	GNRHR	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:68652800-68675000	Weak transcription	Gastric	stomach
2	chr4:68668600-68677200	Weak transcription	Right Ventricle	heart
3	chr4:68669000-68678000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:68669400-68674800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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