Variant report

Variant	rs28480058
Chromosome Location	chr5:89899704-89899705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
2	chr5:89704196..89707423-chr5:89899106..89902473,4	K562	blood:
3	chr5:89898813..89900369-chr5:89978096..89979989,2	K562	blood:
4	chr5:89899642..89902183-chr5:89950994..89955309,3	K562	blood:
5	chr5:89894691..89897119-chr5:89898075..89900513,3	K562	blood:
6	chr5:89767614..89772956-chr5:89898929..89905987,8	K562	blood:
7	chr5:89823952..89826315-chr5:89899219..89901608,2	K562	blood:
8	chr5:89844169..89846312-chr5:89898402..89900420,2	K562	blood:
9	chr5:89897975..89900696-chr5:89937499..89939734,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000176018	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000153140	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12653924	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1316970	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149321	0.99[ASN][1000 genomes]
rs154566	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673381	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs171630	0.80[ASN][1000 genomes]
rs2366772	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2366775	0.96[ASN][1000 genomes]
rs250366	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs250369	0.96[ASN][1000 genomes]
rs27196	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27197	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3112773	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4588621	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5028525	0.95[ASN][1000 genomes]
rs567441	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649449	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs656679	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6891287	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6891840	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6892132	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs908818	0.80[ASN][1000 genomes]
rs9283789	0.90[ASN][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	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28480058	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89892800-89909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:89893000-89907800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:89893200-89902000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:89895000-89907400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:89895800-89899800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:89899000-89900800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr5:89899200-89900800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:89899200-89901000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:89899400-89900400	Weak transcription	K562	blood
10	chr5:89899600-89900600	Weak transcription	GM12878-XiMat	blood
11	chr5:89899600-89902000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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