Variant report

Variant	rs2754813
Chromosome Location	chr6:54074482-54074483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456171	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10948810	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1150873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11757700	0.81[CEU][hapmap]
rs12195488	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12198031	1.00[CHB][hapmap]
rs12198070	1.00[CHB][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap]
rs12201103	1.00[JPT][hapmap]
rs12201129	0.91[EUR][1000 genomes]
rs12201557	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12206177	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12208501	1.00[JPT][hapmap]
rs12212572	0.90[EUR][1000 genomes]
rs12212836	1.00[JPT][hapmap]
rs12214345	0.91[EUR][1000 genomes]
rs12215211	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12333151	1.00[CHD][hapmap]
rs1298143	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1340660	1.00[JPT][hapmap]
rs1417390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16885122	1.00[CHB][hapmap]
rs16885246	1.00[JPT][hapmap]
rs17681477	1.00[CHD][hapmap];0.92[GIH][hapmap]
rs1934790	1.00[CHB][hapmap]
rs2066205	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2180931	0.80[CEU][hapmap]
rs2297980	1.00[JPT][hapmap]
rs2754786	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2754809	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2754812	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2792644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2792656	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3957360	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4712059	0.81[CEU][hapmap]
rs6905414	0.91[EUR][1000 genomes]
rs6937514	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6939568	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs816370	0.85[CEU][hapmap]
rs816371	0.85[CEU][hapmap]
rs816382	0.86[CEU][hapmap]
rs816383	0.80[CEU][hapmap]
rs816385	0.81[CEU][hapmap]
rs843827	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9349700	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9370276	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9382311	0.92[CEU][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9395920	0.92[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9464035	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv603110	chr6:53885918-54103794	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017633	chr6:53935336-54118476	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv981145	chr6:54074450-54075445	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2754813	GSTA1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53998000-54099200	Weak transcription	Psoas Muscle	Psoas
2	chr6:54058800-54101000	Weak transcription	Left Ventricle	heart
3	chr6:54070200-54098800	Weak transcription	Fetal Heart	heart
4	chr6:54070400-54095200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:54072600-54075000	Weak transcription	HepG2	liver

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