Variant report

Variant	rs977576
Chromosome Location	chr5:52557210-52557211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52556927..52559898-chr5:53605181..53607975,2	K562	blood:
2	chr5:52555362..52559874-chr5:52773388..52777640,5	MCF-7	breast:
3	chr5:52557126..52559767-chr7:94821707..94823936,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction
ENSG00000134363	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1025027	0.84[EUR][1000 genomes]
rs10940307	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13171110	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13175197	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1363919	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1363920	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1392541	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423422	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs153618	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153619	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17242004	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs192262	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs254146	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs254198	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs254199	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs254503	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548321	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34721303	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3910971	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39860	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865543	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865762	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865763	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4865764	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57244200	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67239762	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7722242	0.86[ASN][1000 genomes]
rs7737693	0.92[ASN][1000 genomes]
rs7737805	0.90[ASN][1000 genomes]
rs977575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830297	chr5:52492494-52707758	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv522454	chr5:52492677-52571758	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs977576	GZMK	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52541800-52559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:52548600-52561400	Enhancers	HMEC	breast
3	chr5:52550000-52558800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:52553600-52558800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:52555400-52559800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:52556400-52558000	Enhancers	Osteobl	bone
7	chr5:52556600-52559600	Enhancers	NHDF-Ad	bronchial
8	chr5:52556600-52561400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:52556800-52557600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:52557000-52557400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:52557000-52557600	Enhancers	HSMM	muscle
12	chr5:52557000-52558600	Weak transcription	NHEK	skin
13	chr5:52557000-52559200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:52557000-52559400	Enhancers	NHLF	lung
15	chr5:52557200-52557400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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