Variant report

Variant	rs1423422
Chromosome Location	chr5:52631507-52631508
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	chr5:52557875..52558873-chr5:52630604..52631511,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10940307	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13167016	0.81[ASN][1000 genomes]
rs13171110	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13175197	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1363919	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1363920	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3910971	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4865543	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs4865762	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865763	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865764	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57244200	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67239762	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7737693	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7737805	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs977575	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs977576	0.83[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1020388	chr5:52607736-52637122	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv1016368	chr5:52607736-52640986	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv1027244	chr5:52631507-52644776	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1423422	GZMK	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52620200-52633600	Weak transcription	Esophagus	oesophagus
2	chr5:52626000-52631600	Enhancers	NHLF	lung
3	chr5:52626000-52640000	Enhancers	HMEC	breast
4	chr5:52626200-52631600	Enhancers	NHDF-Ad	bronchial
5	chr5:52626400-52631800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:52626600-52631600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:52626800-52631600	Enhancers	Osteobl	bone
8	chr5:52629000-52631600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:52629000-52631600	Enhancers	Hela-S3	cervix
10	chr5:52629000-52631600	Enhancers	HSMM	muscle
11	chr5:52629200-52632000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:52629600-52632000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:52629600-52634000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:52629800-52631600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:52630000-52633800	Enhancers	NHEK	skin
16	chr5:52630200-52631600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr5:52630400-52631600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:52630800-52631800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:52631200-52633800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:52631400-52633800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:52631400-52634600	Weak transcription	Aorta	Aorta

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