Variant report

Variant	rs517190
Chromosome Location	chr15:29697833-29697834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1093564	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12185114	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491720	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs510624	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs538077	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs554755	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs581372	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585137	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs621080	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs646262	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs686122	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167288	0.91[AFR][1000 genomes]
rs818089	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs818091	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv3364436	chr15:29459739-29853229	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs517190	APBA2	cis	parietal	SCAN
rs517190	SNORD116-14	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29694200-29701800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr15:29694200-29702000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:29694200-29702000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:29694200-29702000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:29694400-29702000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:29696600-29701800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:29696800-29702000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:29696800-29704000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:29697000-29701800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:29697200-29701800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:29697800-29698000	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:29697800-29698000	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:29697800-29698000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:29697800-29698000	Enhancers	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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