Variant report

Variant	rs10821409
Chromosome Location	chr9:93173645-93173646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93141218..93144173-chr9:93173013..93175871,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10761373	0.81[JPT][hapmap]
rs10821444	0.82[JPT][hapmap]
rs10821452	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10993468	0.81[JPT][hapmap]
rs10993469	0.81[JPT][hapmap]
rs1426507	0.81[CHB][hapmap]
rs1529333	0.88[MEX][hapmap]
rs1777035	0.91[JPT][hapmap]
rs1930923	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs2771080	0.91[JPT][hapmap]
rs2771081	0.91[JPT][hapmap]
rs3748185	0.82[JPT][hapmap]
rs3748186	0.82[JPT][hapmap]
rs3748187	0.82[JPT][hapmap]
rs6479595	0.82[JPT][hapmap]
rs7029610	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs7046597	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7047032	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs7870764	0.82[JPT][hapmap]
rs9332454	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3483705	chr9:93162382-93194535	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3483706	chr9:93162396-93194531	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3483981	chr9:93172306-93175296	Active TSS Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv3483982	chr9:93172306-93175296	Active TSS ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10821409	IARS	cis	parietal	SCAN
rs10821409	RP11-389K14.3	cis	lung	GTEx
rs10821409	LOC440173	cis	cerebellum	SCAN
rs10821409	SPTLC1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93169600-93174600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:93171200-93180800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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