Variant report

Variant	rs6560517
Chromosome Location	chr9:79038170-79038171
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10119532	0.94[GIH][hapmap]
rs10121699	0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10124695	0.87[ASN][1000 genomes]
rs10781361	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10869767	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869773	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144864	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11144865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11144866	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11144871	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144880	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11144898	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11788095	0.86[ASN][1000 genomes]
rs12057052	0.80[ASN][1000 genomes]
rs13295433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13302654	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1535845	0.87[ASN][1000 genomes]
rs1961995	0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2002423	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2251604	0.95[ASN][1000 genomes]
rs2377639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2490572	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2490573	0.91[ASN][1000 genomes]
rs2490576	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2490579	0.95[ASN][1000 genomes]
rs2490583	0.83[ASN][1000 genomes]
rs2490584	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2490586	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2501920	0.82[ASN][1000 genomes]
rs2501922	0.93[ASN][1000 genomes]
rs2501923	0.95[ASN][1000 genomes]
rs2501925	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2501927	0.95[ASN][1000 genomes]
rs2501928	0.93[ASN][1000 genomes]
rs2501930	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2501933	0.91[ASN][1000 genomes]
rs2501935	0.91[ASN][1000 genomes]
rs35837300	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3739516	0.80[CEU][hapmap]
rs3739729	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4372070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4745541	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4745544	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4745545	0.83[ASN][1000 genomes]
rs4745546	0.82[ASN][1000 genomes]
rs4745549	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4745551	0.91[GIH][hapmap]
rs4745552	0.80[CEU][hapmap];0.94[GIH][hapmap]
rs6560522	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs7847608	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7849239	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871849	0.94[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Dialysis-related mortality	21546767	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6560517	VPS13A	cis	parietal	SCAN
rs6560517	RFK	cis	parietal	SCAN
rs6560517	GNA14	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79030400-79038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr9:79032400-79038200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:79033000-79038200	Weak transcription	Primary T cells from cord blood	blood
4	chr9:79034800-79046000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:79035000-79038800	Weak transcription	Stomach Mucosa	stomach
6	chr9:79036800-79039200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:79037400-79039400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:79038000-79038400	Enhancers	Ovary	ovary
9	chr9:79038000-79038400	Flanking Active TSS	HepG2	liver
10	chr9:79038000-79038600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr9:79038000-79046800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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