Variant report

Variant	rs28001
Chromosome Location	chr5:106830766-106830767
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs152562	0.84[EUR][1000 genomes]
rs25966	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs25969	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs25972	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs25979	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs25980	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs25981	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs25982	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs25996	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs25997	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs26236	0.83[EUR][1000 genomes]
rs26240	0.83[EUR][1000 genomes]
rs27853	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs31717	0.94[EUR][1000 genomes]
rs32013	0.82[EUR][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	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106808400-106837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:106820600-106838200	Weak transcription	Fetal Brain Male	brain
3	chr5:106822800-106832200	Weak transcription	HSMM	muscle
4	chr5:106823000-106834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:106823000-106837600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:106823200-106832600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:106823200-106837800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:106823400-106835400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:106823600-106834400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:106823600-106837800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:106823800-106834000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:106823800-106834200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:106823800-106835000	Weak transcription	A549	lung
14	chr5:106825800-106832000	Weak transcription	Right Atrium	heart
15	chr5:106825800-106835400	Weak transcription	HUVEC	blood vessel
16	chr5:106826600-106838400	Weak transcription	Left Ventricle	heart
17	chr5:106828600-106834200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:106829600-106830800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:106829600-106834000	Weak transcription	Stomach Mucosa	stomach
20	chr5:106829600-106834200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:106829600-106834400	Weak transcription	Fetal Heart	heart
22	chr5:106829600-106837600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:106829800-106831400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:106829800-106835800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:106830600-106837800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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