Variant report

Variant	rs10940601
Chromosome Location	chr5:57487472-57487473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57476926..57490322-chr5:57753628..57758155,26	MCF-7	breast:
2	chr5:57485425..57487725-chr5:57748196..57751309,3	MCF-7	breast:
3	chr5:57485569..57487719-chr5:57497536..57499208,2	MCF-7	breast:
4	chr5:57481839..57487904-chr5:57753425..57757545,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10940600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960642	0.89[EUR][1000 genomes]
rs12521574	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13163245	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13173077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13173083	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13178618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13180583	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1473199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2052545	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112905	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2194194	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216681	0.85[AMR][1000 genomes]
rs2910568	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs2910595	0.85[AMR][1000 genomes]
rs2910597	0.81[ASW][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2910608	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs2962006	0.92[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap]
rs2962014	0.93[ASW][hapmap]
rs2964179	0.90[EUR][1000 genomes]
rs2964181	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2964189	0.93[ASW][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.84[AMR][1000 genomes]
rs35057576	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35133491	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6450469	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6873296	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6876418	0.80[GIH][hapmap]
rs6889867	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6891650	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7446005	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs764629	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs7734713	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv969959	chr5:57486620-57495174	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10940601	GZMA	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57483000-57488400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:57484200-57488200	Enhancers	Hela-S3	cervix
3	chr5:57484600-57487600	Flanking Active TSS	A549	lung
4	chr5:57485400-57487800	Weak transcription	Adipose Nuclei	Adipose
5	chr5:57485800-57490400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:57486000-57488200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:57486800-57488000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:57487000-57487600	Enhancers	Brain Hippocampus Middle	brain
9	chr5:57487000-57487800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:57487200-57487600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:57487200-57488200	Enhancers	HMEC	breast
12	chr5:57487400-57487600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:57487400-57488000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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