Variant report

Variant	rs16897420
Chromosome Location	chr6:28782998-28782999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs9257148	0.81[EUR][1000 genomes]
rs9257168	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9257185	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9257260	0.90[EUR][1000 genomes]
rs9257316	0.81[EUR][1000 genomes]
rs9257319	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv9558	chr6:28770281-28785058	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3410540	chr6:28770455-28785112	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3322630	chr6:28770519-28785092	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3486939	chr6:28770525-28785051	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3486940	chr6:28770525-28785051	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3403106	chr6:28770790-28785189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv970724	chr6:28778144-28784760	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16897420	PGBD1	cis	cerebellum	SCAN
rs16897420	HIST1H2AE	cis	parietal	SCAN
rs16897420	ZNF391	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28782400-28783200	Bivalent Enhancer	HepG2	liver
2	chr6:28782400-28784000	Weak transcription	HMEC	breast
3	chr6:28782600-28783000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
4	chr6:28782600-28783000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr6:28782600-28783000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr6:28782600-28783800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr6:28782600-28784000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr6:28782600-28784000	Enhancers	K562	blood
9	chr6:28782800-28783000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr6:28782800-28783000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr6:28782800-28783600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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