Variant report

Variant	rs9823785
Chromosome Location	chr3:141061438-141061439
allele	A/G
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:14)

rs_ID	r²[population]
rs13063736	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13095453	0.84[CEU][hapmap];0.93[GIH][hapmap];0.81[YRI][hapmap]
rs13324219	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13434224	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1511380	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs4325905	0.88[CEU][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs4536797	0.81[AMR][1000 genomes]
rs6765238	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs6785073	0.80[CEU][hapmap]
rs726838	0.84[CEU][hapmap]
rs7616781	0.88[CEU][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs9823774	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9829470	0.92[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9857275	0.84[CEU][hapmap];0.93[GIH][hapmap]

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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9823785	RASA2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141056400-141061600	Weak transcription	Small Intestine	intestine
2	chr3:141056400-141079400	Weak transcription	A549	lung
3	chr3:141056600-141064200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:141056600-141064800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:141057800-141061800	Weak transcription	HepG2	liver
6	chr3:141058200-141061800	Weak transcription	Liver	Liver
7	chr3:141058200-141065000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:141059800-141063000	Enhancers	K562	blood
9	chr3:141061400-141061800	Genic enhancers	Fetal Intestine Small	intestine
10	chr3:141061400-141062000	Enhancers	Fetal Intestine Large	intestine
11	chr3:141061400-141064400	Enhancers	Duodenum Mucosa	Duodenum

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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