Variant report

Variant	rs4285175
Chromosome Location	chr5:57139075-57139076
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	chr5:57138883..57141351-chr5:57755276..57756971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10072292	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1821210	1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1861059	1.00[MKK][hapmap];0.81[TSI][hapmap];0.84[AFR][1000 genomes]
rs2408854	0.95[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568537	0.84[AFR][1000 genomes]
rs4235475	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4235476	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	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4380607	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4403130	0.95[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4421067	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4458541	0.95[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4513644	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4699913	0.81[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4700231	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4700233	0.81[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6450442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450444	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6896848	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs702699	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs702701	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7701200	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7724301	0.80[CEU][hapmap]
rs854024	0.84[AFR][1000 genomes]
rs854028	0.84[AFR][1000 genomes]
rs854031	0.84[AFR][1000 genomes]
rs854033	0.84[AFR][1000 genomes]
rs854035	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs854036	0.85[CEU][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs854038	0.82[AMR][1000 genomes]
rs854039	0.81[AMR][1000 genomes]
rs854042	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs854045	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs854046	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs854048	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs854049	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs854050	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs854052	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs854053	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs868049	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs897264	0.97[AMR][1000 genomes];0.95[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
rs4285175	GZMK	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57130200-57139200	Enhancers	HMEC	breast
2	chr5:57131400-57140000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:57131400-57141000	Weak transcription	Left Ventricle	heart
4	chr5:57136800-57141200	Enhancers	Fetal Muscle Leg	muscle
5	chr5:57137600-57142800	Weak transcription	Fetal Brain Male	brain
6	chr5:57137800-57141000	Weak transcription	Right Ventricle	heart
7	chr5:57138000-57140200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:57138000-57143000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:57138200-57139200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:57138200-57139200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:57138200-57139400	Weak transcription	Placenta	Placenta
12	chr5:57138200-57139400	Enhancers	Osteobl	bone
13	chr5:57138200-57139800	Enhancers	HSMM	muscle
14	chr5:57138200-57141000	Enhancers	NHEK	skin
15	chr5:57138200-57142800	Weak transcription	Fetal Lung	lung
16	chr5:57138200-57143600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:57138400-57139400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:57138400-57140400	Weak transcription	Adipose Nuclei	Adipose
19	chr5:57138400-57140400	Weak transcription	Brain Germinal Matrix	brain
20	chr5:57138400-57143400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:57138600-57141200	Enhancers	HUVEC	blood vessel
22	chr5:57138800-57139600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:57138800-57142600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:57138800-57151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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