Variant report

Variant	rs4719842
Chromosome Location	chr7:25999018-25999019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10252380	0.85[ASN][1000 genomes]
rs10279044	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12700685	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs13235988	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs4719843	0.80[ASN][1000 genomes]
rs4719844	0.80[ASN][1000 genomes]
rs4722554	0.81[ASN][1000 genomes]
rs4722561	0.85[ASN][1000 genomes]
rs6947992	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6958870	0.84[MEX][hapmap]
rs6968046	0.89[ASN][1000 genomes]
rs766839	0.83[ASN][1000 genomes]
rs9638829	0.83[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	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4719842	HOXA3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25994600-26001400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:25998400-25999200	Enhancers	Pancreas	Pancrea
3	chr7:25998600-25999200	Enhancers	HepG2	liver
4	chr7:25998800-25999200	Enhancers	H9 Cell Line	embryonic stem cell
5	chr7:25998800-25999200	Enhancers	Primary B cells from peripheral blood	blood
6	chr7:25998800-25999200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr7:25998800-25999400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr7:25998800-25999400	Enhancers	Liver	Liver
9	chr7:25998800-25999600	Flanking Active TSS	GM12878-XiMat	blood
10	chr7:25999000-26002400	Weak transcription	Spleen	Spleen

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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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