Variant report

Variant	rs154573
Chromosome Location	chr5:89865123-89865124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89864609..89867407-chr5:89868607..89870565,2	K562	blood:
2	chr5:89856963..89860302-chr5:89865083..89868215,3	MCF-7	breast:
3	chr5:89851829..89860351-chr5:89861712..89870170,13	K562	blood:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10069050	0.85[EUR][1000 genomes]
rs154568	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs154569	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154570	0.91[EUR][1000 genomes]
rs154572	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1553545	0.85[EUR][1000 genomes]
rs171790	0.85[EUR][1000 genomes]
rs250377	0.87[EUR][1000 genomes]
rs257850	0.85[EUR][1000 genomes]
rs257851	0.84[EUR][1000 genomes]
rs2656957	0.85[EUR][1000 genomes]
rs27201	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37238	0.85[EUR][1000 genomes]
rs37239	0.80[EUR][1000 genomes]
rs42467	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs43149	0.85[EUR][1000 genomes]
rs491082	0.85[EUR][1000 genomes]
rs511393	0.85[EUR][1000 genomes]
rs526806	0.86[EUR][1000 genomes]
rs556894	0.86[EUR][1000 genomes]
rs594990	0.87[EUR][1000 genomes]
rs599432	0.82[EUR][1000 genomes]
rs679568	0.81[EUR][1000 genomes]
rs810974	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs154573	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89855200-89871000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:89859400-89884200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:89860200-89868000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:89864000-89865600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr5:89864200-89867400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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