Variant report

Variant	rs28474924
Chromosome Location	chr4:95086345-95086346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPGDS-1	chr4:95086287-95086347	ENSG00000246541

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10433970	0.87[EUR][1000 genomes]
rs11097406	0.85[EUR][1000 genomes]
rs11097407	0.86[EUR][1000 genomes]
rs11724791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501826	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12502310	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12502343	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12510326	0.87[EUR][1000 genomes]
rs1605923	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17021364	0.81[EUR][1000 genomes]
rs1828324	0.92[EUR][1000 genomes]
rs1876917	0.88[EUR][1000 genomes]
rs2169719	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2199602	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2632423	0.83[ASN][1000 genomes]
rs28398254	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28417458	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28613890	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28696050	0.87[EUR][1000 genomes]
rs4693000	0.85[EUR][1000 genomes]
rs56161035	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56197713	0.91[EUR][1000 genomes]
rs60428594	0.88[EUR][1000 genomes]
rs61069704	0.91[EUR][1000 genomes]
rs72663782	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72663785	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72663787	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72663802	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv931979	chr4:94289958-95121723	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv821636	chr4:94439636-95116590	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv879618	chr4:94980768-95136164	Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879621	chr4:95046907-95099194	Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95085200-95089800	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr4:95085400-95086400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:95085400-95086800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr4:95085400-95087000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:95085600-95086800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:95085600-95086800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:95085800-95087200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:95086000-95089000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr4:95086200-95086400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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