Variant report

Variant	rs6560519
Chromosome Location	chr9:79047117-79047118
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10114264	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10121699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10124695	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735646	0.87[CHB][hapmap];0.85[EUR][1000 genomes]
rs10781361	0.86[ASN][1000 genomes]
rs10781362	0.99[ASN][1000 genomes]
rs10869780	0.89[EUR][1000 genomes]
rs11144864	0.95[JPT][hapmap]
rs11144865	0.95[JPT][hapmap]
rs11144898	0.87[ASN][1000 genomes]
rs11144899	0.99[ASN][1000 genomes]
rs11788095	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12057052	0.82[EUR][1000 genomes]
rs1535845	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1961995	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs2002423	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs2377639	0.95[JPT][hapmap]
rs2490572	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs2490574	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2490576	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2490583	0.88[AMR][1000 genomes]
rs2490584	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2490586	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2501920	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2501925	0.90[JPT][hapmap]
rs2501930	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap]
rs2501932	0.81[EUR][1000 genomes]
rs2501940	0.80[EUR][1000 genomes]
rs2501942	0.81[EUR][1000 genomes]
rs4372070	0.95[JPT][hapmap]
rs4745544	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4745545	0.91[AMR][1000 genomes]
rs4745546	0.85[AMR][1000 genomes]
rs4745548	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4745549	0.85[ASN][1000 genomes]
rs6560520	1.00[ASN][1000 genomes]
rs6560521	1.00[ASN][1000 genomes]
rs6560522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs7038837	0.96[ASN][1000 genomes]
rs7847608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv3451027	chr9:79021447-79056132	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv520423	chr9:79047117-79065299	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6560519	C9orf40	cis	cerebellum	SCAN
rs6560519	ZSWIM4	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79046000-79047200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr9:79046200-79047200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr9:79046200-79048600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr9:79046400-79047600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:79046400-79047800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:79046400-79047800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:79046400-79048000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:79047000-79047200	Weak transcription	HepG2	liver
9	chr9:79047000-79047400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:79047000-79047800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:79047000-79048000	Weak transcription	H9 Cell Line	embryonic stem cell

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