Variant report

Variant	rs56914580
Chromosome Location	chr5:126739488-126739489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10519940	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11743165	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11743299	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743942	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11747741	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11749174	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11750372	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11750401	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17164929	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17164938	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17684962	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17763370	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839692	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2003863	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2270931	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2860028	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35591368	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3863175	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41298322	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60019013	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73783790	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73783795	1.00[AMR][1000 genomes];0.95[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv526333	chr5:126732427-126746277	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56914580	LOC728586	cis	temporal cortex	BrainEAC

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126691000-126746000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:126710200-126741200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:126720000-126742000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:126731800-126741800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:126731800-126742000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:126732000-126741200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:126732400-126741600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:126732600-126741800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:126734800-126753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:126736200-126741600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:126737000-126742000	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:126737200-126741600	Weak transcription	Brain Anterior Caudate	brain
13	chr5:126737200-126741600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:126737200-126741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:126737200-126742000	Weak transcription	Brain Angular Gyrus	brain
16	chr5:126737600-126742000	Weak transcription	NH-A	brain
17	chr5:126737600-126743200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:126737600-126746400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:126737800-126741600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:126737800-126741800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:126738400-126741600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:126738400-126741600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:126738400-126741800	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:126738400-126742000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:126738400-126743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:126738600-126741600	Weak transcription	Brain Substantia Nigra	brain
27	chr5:126738600-126742000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:126738600-126745000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:126738800-126741400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:126738800-126742000	Weak transcription	HSMMtube	muscle
31	chr5:126738800-126746200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:126739000-126742000	Weak transcription	HSMM	muscle

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