Variant report

Variant	rs16920439
Chromosome Location	chr9:104264540-104264541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr9:104264376-104264649	GM12878	blood:	n/a	chr9:104264517-104264530 chr9:104264458-104264465 chr9:104264517-104264530 chr9:104264518-104264531

Variant related genes	Relation type
ENSG00000233055	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10819945	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs1113384	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1124148	0.82[ASN][1000 genomes]
rs12005425	0.91[JPT][hapmap]
rs12683273	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12684621	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12684773	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12685862	0.82[ASN][1000 genomes]
rs1407868	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs16920420	0.81[JPT][hapmap]
rs16920438	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs16920447	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs1929484	0.82[ASN][1000 genomes]
rs2150737	0.82[ASN][1000 genomes]
rs4097641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4743465	0.82[ASN][1000 genomes]
rs56357103	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56682764	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57053192	0.81[ASN][1000 genomes]
rs62575809	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575838	0.85[EUR][1000 genomes]
rs68067101	0.99[ASN][1000 genomes]
rs68114463	0.96[ASN][1000 genomes]
rs72743387	0.81[ASN][1000 genomes]
rs72743390	0.81[ASN][1000 genomes]
rs72743393	1.00[ASN][1000 genomes]
rs72743397	0.82[ASN][1000 genomes]
rs7867496	0.91[JPT][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs7873168	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16920439	C9orf30	cis	cerebellum	SCAN
rs16920439	TMEM101	trans	parietal	SCAN
rs16920439	LOC57653	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104263200-104275600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links