Variant report

Variant	rs13428898
Chromosome Location	chr2:53865584-53865585
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53863876..53866246-chr2:53873113..53875135,2	K562	blood:
2	chr2:53863042..53865954-chr2:54012885..54015128,2	K562	blood:

Variant related genes	Relation type
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10490465	0.96[ASN][1000 genomes]
rs10865275	0.85[EUR][1000 genomes]
rs11682721	0.87[EUR][1000 genomes]
rs11889094	0.86[EUR][1000 genomes]
rs11900355	0.97[ASN][1000 genomes]
rs13428687	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045037	0.96[ASN][1000 genomes]
rs17045048	0.96[ASN][1000 genomes]
rs17045081	0.91[ASN][1000 genomes]
rs17045084	0.89[ASN][1000 genomes]
rs2080715	0.85[EUR][1000 genomes]
rs34408637	0.90[ASN][1000 genomes]
rs3731970	0.84[ASN][1000 genomes]
rs3770407	0.85[ASN][1000 genomes]
rs3770408	0.85[ASN][1000 genomes]
rs3770409	0.87[ASN][1000 genomes]
rs3930	0.91[ASN][1000 genomes]
rs55861447	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56056250	0.81[EUR][1000 genomes]
rs56081218	0.99[ASN][1000 genomes]
rs56081372	0.87[EUR][1000 genomes]
rs56311225	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56383522	0.91[ASN][1000 genomes]
rs58125503	0.96[ASN][1000 genomes]
rs58515086	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs60282090	0.89[ASN][1000 genomes]
rs61671599	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62139773	0.96[ASN][1000 genomes]
rs62139774	0.91[ASN][1000 genomes]
rs62139775	0.91[ASN][1000 genomes]
rs62139785	0.91[ASN][1000 genomes]
rs62139788	0.89[ASN][1000 genomes]
rs62139836	0.88[ASN][1000 genomes]
rs6713107	0.83[EUR][1000 genomes]
rs6727876	0.85[EUR][1000 genomes]
rs6728355	0.85[EUR][1000 genomes]
rs6741239	0.80[EUR][1000 genomes]
rs6757393	0.87[EUR][1000 genomes]
rs72901209	0.88[ASN][1000 genomes]
rs73934971	0.81[ASN][1000 genomes]
rs7556791	0.82[EUR][1000 genomes]
rs7600981	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv874145	chr2:53772561-53867308	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv874146	chr2:53772561-53872803	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv874147	chr2:53772561-53886799	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2762637	chr2:53783253-53871596	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv527830	chr2:53785037-53867308	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1008117	chr2:53791985-53869651	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535719	chr2:53791985-53869651	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
11	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13428898	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53857400-53868600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:53865000-53868000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:53865000-53870000	Weak transcription	Fetal Brain Male	brain

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