Variant report

Variant	rs854050
Chromosome Location	chr5:57106067-57106068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57105712..57108165-chr5:57110321..57113589,3	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10057880	1.00[YRI][hapmap]
rs10072292	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1347071	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1821210	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1861059	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2408854	1.00[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2568537	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2568549	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4235475	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4235476	0.89[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4285175	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4317282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4380607	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4403130	1.00[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4421067	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4458541	1.00[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4513644	0.91[AFR][1000 genomes]
rs4699913	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4700231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700233	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs62362089	0.82[AFR][1000 genomes]
rs6450442	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6450444	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6896848	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs702699	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs702700	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs702701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71585052	0.80[EUR][1000 genomes]
rs7701200	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7724301	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs854024	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs854028	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs854031	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs854033	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs854035	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854036	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854038	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs854039	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854045	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs854046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs854052	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868049	0.84[AFR][1000 genomes]
rs897264	0.88[AMR][1000 genomes];0.81[EUR][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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs854050	GZMK	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57100600-57111600	Weak transcription	HSMM	muscle
2	chr5:57101600-57111600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:57102400-57107600	Weak transcription	Osteobl	bone
4	chr5:57102400-57108000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr5:57102400-57108000	Weak transcription	NHDF-Ad	bronchial
6	chr5:57102400-57112000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:57105200-57107200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:57105600-57112200	Weak transcription	NHLF	lung

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