Variant report

Variant	rs677887
Chromosome Location	chr18:29818150-29818151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11081752	0.95[ASN][1000 genomes]
rs1561815	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1561816	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs16962815	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs16962818	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4799330	0.90[ASN][1000 genomes]
rs4799641	0.91[ASN][1000 genomes]
rs616114	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs625188	0.98[ASN][1000 genomes]
rs673408	0.80[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs679163	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs680321	0.83[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7233927	0.89[ASN][1000 genomes]
rs9953120	0.90[ASN][1000 genomes]
rs9965114	0.97[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	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs677887	CHST9	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29814200-29818400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr18:29814200-29819000	Enhancers	Fetal Intestine Large	intestine
3	chr18:29816400-29818800	Weak transcription	Aorta	Aorta
4	chr18:29817600-29822200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr18:29818000-29818800	Enhancers	Fetal Intestine Small	intestine

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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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