Variant report

Variant	rs7853235
Chromosome Location	chr9:86660782-86660783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10746729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10780643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10780644	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10780645	1.00[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs167203	0.92[CEU][hapmap]
rs296886	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap]
rs296894	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs55692426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55714514	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7853377	0.92[CEU][hapmap]
rs930340	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv614762	chr9:86625243-86700593	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7853235	LOC440173	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86660000-86661000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86660000-86661000	Enhancers	Placenta	Placenta
3	chr9:86660200-86660800	Enhancers	Spleen	Spleen
4	chr9:86660400-86660800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:86660600-86661000	Enhancers	H1 Cell Line	embryonic stem cell
6	chr9:86660600-86661000	Flanking Active TSS	HepG2	liver
7	chr9:86660600-86661200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr9:86660600-86661200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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