Variant report

Variant	rs4235476
Chromosome Location	chr5:57156597-57156598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57155155..57158573-chr5:57754474..57756778,3	MCF-7	breast:
2	chr5:57155875..57158206-chr5:57754452..57757615,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10072292	0.87[EUR][1000 genomes]
rs1821210	0.90[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs2408854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235475	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285175	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4317282	0.85[EUR][1000 genomes]
rs4380607	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4403130	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4421067	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458541	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4513644	0.85[EUR][1000 genomes]
rs4699913	0.91[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4700231	0.85[EUR][1000 genomes]
rs4700233	0.91[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6450442	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450444	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6896848	0.83[EUR][1000 genomes]
rs702699	0.83[EUR][1000 genomes]
rs702701	0.83[EUR][1000 genomes]
rs7701200	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs854042	0.83[EUR][1000 genomes]
rs854046	0.83[EUR][1000 genomes]
rs854048	0.83[EUR][1000 genomes]
rs854049	0.83[EUR][1000 genomes]
rs854050	0.83[EUR][1000 genomes]
rs854052	0.85[EUR][1000 genomes]
rs854053	0.85[EUR][1000 genomes]
rs868049	0.87[EUR][1000 genomes]
rs897264	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][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
rs4235476	GZMK	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57151200-57158200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:57151400-57160000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:57154000-57157200	Weak transcription	HMEC	breast
4	chr5:57155000-57157600	Weak transcription	Fetal Heart	heart
5	chr5:57155200-57156800	Enhancers	NHEK	skin
6	chr5:57155200-57158200	Weak transcription	Fetal Lung	lung
7	chr5:57155400-57156800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:57155400-57158400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:57155600-57157600	Weak transcription	HSMM	muscle
10	chr5:57155600-57158200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:57155600-57159200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:57156000-57160000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr5:57156200-57159800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:57156400-57160600	Enhancers	Placenta	Placenta

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