Variant report

Variant	rs9403825
Chromosome Location	chr6:147218450-147218451
allele	C/T
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:10)

rs_ID	r²[population]
rs1998641	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs4895704	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724774	0.88[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs912577	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377035	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390435	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399586	0.83[CEU][hapmap]
rs9399589	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9399590	0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9403828	0.86[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	nsv830838	chr6:147090745-147274669	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv442012	chr6:147210681-147219817	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9403825	KATNA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147215000-147219200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:147215200-147219600	Flanking Active TSS	K562	blood
3	chr6:147215200-147224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:147216000-147224600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:147216800-147220000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:147217000-147220400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:147217000-147220400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:147217400-147220600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:147218000-147225800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:147218200-147226600	Weak transcription	NHLF	lung

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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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