Variant report

Variant	rs331716
Chromosome Location	chr5:124895737-124895738
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:124893901..124896559-chr5:124897191..124899383,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10434773	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10434774	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1457711	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2125138	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2608114	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2608115	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2608117	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2637503	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2925892	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs330336	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs330337	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs330338	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs330341	0.84[AMR][1000 genomes]
rs330343	0.84[AMR][1000 genomes]
rs330344	0.84[AMR][1000 genomes]
rs330350	0.80[AMR][1000 genomes]
rs330352	0.80[AMR][1000 genomes]
rs330353	0.80[AMR][1000 genomes]
rs330355	0.80[AMR][1000 genomes]
rs330356	0.80[AMR][1000 genomes]
rs331704	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs331705	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs331709	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs331710	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs331711	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs331712	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs331713	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs331714	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs331720	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs331721	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs331724	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs331725	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs331773	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6896312	0.81[AMR][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	nsv1030992	chr5:124708549-125391503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv537892	chr5:124708549-125391503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv882827	chr5:124867823-124943901	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv882828	chr5:124867823-124958205	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs331716	PHAX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124893600-124896800	Enhancers	Stomach Mucosa	stomach
2	chr5:124893800-124895800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:124893800-124896000	Enhancers	HSMM	muscle
4	chr5:124893800-124896600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:124893800-124896600	Enhancers	HUVEC	blood vessel
6	chr5:124893800-124896800	Enhancers	HMEC	breast
7	chr5:124893800-124896800	Enhancers	NHEK	skin
8	chr5:124894000-124896600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:124894000-124896600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:124894200-124895800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:124894200-124897000	Enhancers	Osteobl	bone
12	chr5:124894400-124895800	Enhancers	Fetal Heart	heart
13	chr5:124894400-124896400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:124894400-124896800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:124894400-124897200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:124894800-124896000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:124894800-124896600	Enhancers	NHDF-Ad	bronchial
18	chr5:124894800-124896800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:124894800-124896800	Enhancers	NHLF	lung
20	chr5:124895000-124895800	Enhancers	A549	lung
21	chr5:124895000-124896000	Enhancers	Hela-S3	cervix
22	chr5:124895000-124896600	Enhancers	Gastric	stomach
23	chr5:124895000-124897000	Enhancers	NH-A	brain
24	chr5:124895600-124895800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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