Variant report

Variant	rs12597800
Chromosome Location	chr16:76235264-76235265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11149879	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11149880	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11149881	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11859283	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11863642	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11863922	0.82[EUR][1000 genomes]
rs12447696	0.92[AMR][1000 genomes]
rs12596390	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12597719	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12597760	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12599008	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12599976	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34644374	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3844220	0.94[AMR][1000 genomes]
rs3844221	0.94[AMR][1000 genomes]
rs3851748	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3851749	0.90[AMR][1000 genomes]
rs3851750	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3851752	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3902005	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4122328	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41363750	0.80[ASN][1000 genomes]
rs41515248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4614753	0.81[CHB][hapmap]
rs4888481	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4888482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4888483	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4888484	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56101390	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56331613	0.94[AMR][1000 genomes]
rs56349355	0.92[AMR][1000 genomes]
rs56802647	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61005161	0.92[AMR][1000 genomes]
rs61092055	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61464757	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9635569	0.82[EUR][1000 genomes]
rs9635570	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1064607	chr16:75787129-76449101	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1065794	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv542961	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1059162	chr16:75929348-76730816	Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv572995	chr16:75935025-76708417	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv572996	chr16:75935025-76735249	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv817220	chr16:75939705-76735383	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1056021	chr16:75955522-76729765	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv542962	chr16:75955522-76729765	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv906935	chr16:76031737-76453110	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv906936	chr16:76031737-76768178	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv817549	chr16:76067068-76582099	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv833285	chr16:76136345-76345398	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1065644	chr16:76166579-76475634	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv573002	chr16:76174188-76280843	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv906938	chr16:76174188-76293092	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv906939	chr16:76188497-76277895	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv869200	chr16:76227867-76695732	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12597800	ADAT1	cis	parietal	SCAN
rs12597800	HYDIN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:76229000-76235400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr16:76229200-76241200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:76233600-76235400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr16:76233800-76235400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:76233800-76235400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr16:76233800-76236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:76234000-76235400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr16:76234400-76236800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr16:76234800-76236600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr16:76235200-76236000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr16:76235200-76236000	Enhancers	HMEC	breast
12	chr16:76235200-76236400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr16:76235200-76236400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr16:76235200-76236600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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