Variant report

Variant	rs55875824
Chromosome Location	chr5:179596768-179596769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10044602	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10063012	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10068846	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10069716	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10070065	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10077265	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10077711	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10078112	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10078173	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10079475	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28455061	0.84[EUR][1000 genomes]
rs28592916	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28811617	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55808016	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56250501	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406101	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72813675	0.84[EUR][1000 genomes]
rs7447697	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs882701	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer 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 miRNA target site	189 gene(s)	inside rSNPs	diseases
2	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
4	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
5	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv883288	chr5:179537727-179608656	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv1030036	chr5:179543546-179610871	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv830562	chr5:179555313-179622441	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 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	chr5:179589400-179596800	Weak transcription	Brain Angular Gyrus	brain
2	chr5:179594400-179596800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr5:179595000-179596800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:179595400-179597400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr5:179595600-179596800	Enhancers	Fetal Muscle Trunk	muscle
6	chr5:179595600-179597000	Enhancers	Fetal Muscle Leg	muscle
7	chr5:179595600-179597200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr5:179595600-179597600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:179595600-179597800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:179595800-179597000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr5:179595800-179597200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:179595800-179597400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr5:179595800-179600000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:179596000-179597000	Weak transcription	Brain Substantia Nigra	brain
15	chr5:179596000-179598200	Enhancers	Fetal Stomach	stomach
16	chr5:179596200-179597200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:179596200-179597600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr5:179596200-179597800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:179596200-179598400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:179596200-179598400	Enhancers	Primary hematopoietic stem cells	blood
21	chr5:179596400-179597000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:179596400-179597800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:179596400-179598000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr5:179596400-179602200	Enhancers	Fetal Brain Male	brain
25	chr5:179596600-179596800	Enhancers	Brain Hippocampus Middle	brain

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