Variant report

Variant	rs330343
Chromosome Location	chr5:124914520-124914521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10434773	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10434774	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2608114	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2608115	0.90[AMR][1000 genomes]
rs330336	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs330337	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs330338	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs330341	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs330344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330350	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330352	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330353	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330354	0.81[ASN][1000 genomes]
rs330355	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs330356	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs331716	0.84[AMR][1000 genomes]
rs331720	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs331721	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs68142408	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6896312	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv4986	chr5:124899753-124944916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs330343	PHAX	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124908800-124914800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr5:124911600-124917000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:124911800-124914800	Weak transcription	HSMM	muscle
4	chr5:124912000-124916800	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:124912000-124917400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:124912000-124929600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:124912200-124917400	Weak transcription	Fetal Brain Male	brain
8	chr5:124912200-124917600	Weak transcription	HSMMtube	muscle
9	chr5:124912600-124915000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:124912800-124916800	Weak transcription	Fetal Lung	lung
11	chr5:124912800-124917200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:124912800-124917200	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:124912800-124917400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:124912800-124917400	Weak transcription	Brain Angular Gyrus	brain
15	chr5:124912800-124917800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:124912800-124919600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:124913000-124917400	Weak transcription	Brain Germinal Matrix	brain
18	chr5:124913000-124917400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:124913400-124917400	Weak transcription	Osteobl	bone
20	chr5:124914200-124914600	Enhancers	Muscle Satellite Cultured Cells	--

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