Variant report

Variant	rs9474976
Chromosome Location	chr6:54594349-54594350
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54591002..54596706-chr6:54709941..54714732,14	MCF-7	breast:
2	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
3	chr6:54588605..54590894-chr6:54594243..54596836,3	MCF-7	breast:
4	chr6:54589684..54593022-chr6:54593846..54596999,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10085187	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1018140	0.91[ASN][1000 genomes]
rs1039694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1039695	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10738112	0.84[ASN][1000 genomes]
rs10738113	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10807478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948832	0.91[ASN][1000 genomes]
rs12210278	0.91[ASN][1000 genomes]
rs12662500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280714	0.81[ASN][1000 genomes]
rs1280716	0.81[ASN][1000 genomes]
rs1354308	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1393859	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1395626	0.94[ASN][1000 genomes]
rs1415875	0.84[ASN][1000 genomes]
rs1507111	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1572594	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1827514	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1830662	0.81[ASN][1000 genomes]
rs1983141	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2047828	0.81[ASN][1000 genomes]
rs2297805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4094928	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4106094	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712067	0.82[CHB][hapmap]
rs4715465	0.84[ASN][1000 genomes]
rs4715471	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4715472	0.91[CEU][hapmap]
rs4715473	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs542639	0.88[ASN][1000 genomes]
rs58010645	0.97[ASN][1000 genomes]
rs62414317	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6459022	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906010	0.97[ASN][1000 genomes]
rs6907631	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs6909103	0.94[ASN][1000 genomes]
rs6916459	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6928097	0.84[ASN][1000 genomes]
rs6934405	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739195	0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7739425	0.90[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7747427	0.98[ASN][1000 genomes]
rs7759470	0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs7759660	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7770733	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7771107	0.84[ASN][1000 genomes]
rs7772650	0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7773277	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925053	0.95[ASN][1000 genomes]
rs925054	0.97[ASN][1000 genomes]
rs9296758	0.88[CHD][hapmap]
rs9296765	0.94[ASN][1000 genomes]
rs9296767	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370324	0.81[ASN][1000 genomes]
rs9464125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464130	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9464131	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474954	0.94[ASN][1000 genomes]
rs9474975	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9474981	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9474986	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs962307	0.89[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs981683	0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9918378	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv885901	chr6:54588069-54635417	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885902	chr6:54588069-54656673	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9474976	GSTA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54594200-54594400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:54594200-54594800	Enhancers	NHEK	skin
3	chr6:54594200-54595000	Enhancers	HMEC	breast
4	chr6:54594200-54595200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:54594200-54595600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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