Variant report

Variant	rs28725459
Chromosome Location	chr16:31132662-31132663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31132642-31133024	K562	blood:	n/a	n/a
2	POLR2A	chr16:31132346-31132764	K562	blood:	n/a	n/a
3	POLR2A	chr16:31132186-31133474	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:31127220..31133615-chr16:31189948..31195209,18	K562	blood:
2	chr16:30816280..30819245-chr16:31129948..31132814,2	K562	blood:
3	chr16:31132115..31134271-chr16:31191509..31194298,2	K562	blood:

Variant related genes	Relation type
KAT8	TF binding region
ENSG00000260304	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1060506	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1108431	0.81[ASN][1000 genomes]
rs11150604	0.81[ASN][1000 genomes]
rs11642192	0.89[ASN][1000 genomes]
rs11647284	0.91[ASN][1000 genomes]
rs11647442	0.96[ASN][1000 genomes]
rs11862744	0.81[ASN][1000 genomes]
rs11864806	0.91[ASN][1000 genomes]
rs11864839	0.91[ASN][1000 genomes]
rs11865038	0.91[ASN][1000 genomes]
rs11865499	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445650	0.81[ASN][1000 genomes]
rs12448321	0.81[ASN][1000 genomes]
rs12597511	0.93[ASN][1000 genomes]
rs12716981	0.96[ASN][1000 genomes]
rs12716982	0.96[ASN][1000 genomes]
rs12934418	0.81[ASN][1000 genomes]
rs14235	0.96[ASN][1000 genomes]
rs1549293	0.96[ASN][1000 genomes]
rs1549299	0.87[EUR][1000 genomes]
rs17839567	0.81[ASN][1000 genomes]
rs17839568	0.91[ASN][1000 genomes]
rs1978485	0.96[ASN][1000 genomes]
rs1978487	0.96[ASN][1000 genomes]
rs2032915	0.96[ASN][1000 genomes]
rs2288004	0.81[ASN][1000 genomes]
rs2303222	0.91[ASN][1000 genomes]
rs2303223	0.89[ASN][1000 genomes]
rs2359612	0.91[ASN][1000 genomes]
rs2855475	0.96[ASN][1000 genomes]
rs28814987	0.91[ASN][1000 genomes]
rs2884738	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35351013	0.85[ASN][1000 genomes]
rs35468353	0.81[ASN][1000 genomes]
rs35713203	0.91[ASN][1000 genomes]
rs3751855	0.91[ASN][1000 genomes]
rs4468641	0.91[ASN][1000 genomes]
rs4527034	0.96[ASN][1000 genomes]
rs4889619	0.88[ASN][1000 genomes]
rs4889620	0.96[ASN][1000 genomes]
rs55667375	0.83[EUR][1000 genomes]
rs55766044	0.96[ASN][1000 genomes]
rs55979739	0.81[ASN][1000 genomes]
rs56284083	0.81[ASN][1000 genomes]
rs56314408	0.96[ASN][1000 genomes]
rs56813533	0.85[ASN][1000 genomes]
rs57434408	0.82[ASN][1000 genomes]
rs59735493	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60996860	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61162043	0.91[ASN][1000 genomes]
rs61320757	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6565217	0.91[ASN][1000 genomes]
rs7187995	0.85[ASN][1000 genomes]
rs7196161	0.91[ASN][1000 genomes]
rs7196726	0.91[ASN][1000 genomes]
rs7197717	0.91[ASN][1000 genomes]
rs7199949	0.91[ASN][1000 genomes]
rs7294	0.91[ASN][1000 genomes]
rs732172	0.81[ASN][1000 genomes]
rs732173	0.81[ASN][1000 genomes]
rs73530203	0.89[ASN][1000 genomes]
rs749670	0.91[ASN][1000 genomes]
rs749671	0.91[ASN][1000 genomes]
rs749767	0.96[ASN][1000 genomes]
rs7500176	0.81[ASN][1000 genomes]
rs750952	0.91[ASN][1000 genomes]
rs8047803	0.91[ASN][1000 genomes]
rs8050894	0.91[ASN][1000 genomes]
rs8056842	0.81[ASN][1000 genomes]
rs8061047	0.85[ASN][1000 genomes]
rs881929	0.91[ASN][1000 genomes]
rs889548	0.96[ASN][1000 genomes]
rs889555	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9923231	0.91[ASN][1000 genomes]
rs9925964	0.96[ASN][1000 genomes]
rs9934438	0.91[ASN][1000 genomes]
rs9936329	0.96[ASN][1000 genomes]
rs9939417	0.81[ASN][1000 genomes]
rs9939558	0.81[ASN][1000 genomes]
rs9972727	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
6	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
7	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
8	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
9	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
10	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
12	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
13	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28725459	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs28725459	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs28725459	KAT8	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31130000-31132800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:31130200-31133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr16:31130200-31133800	Strong transcription	Brain Germinal Matrix	brain
4	chr16:31130200-31134000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:31130200-31135600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:31130200-31136600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr16:31130400-31133800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr16:31130400-31133800	Strong transcription	Primary hematopoietic stem cells	blood
9	chr16:31130400-31134200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr16:31130400-31134400	Strong transcription	Fetal Lung	lung
11	chr16:31130400-31135800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:31130400-31137200	Weak transcription	Stomach Mucosa	stomach
13	chr16:31130400-31139000	Strong transcription	Fetal Thymus	thymus
14	chr16:31130400-31139800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr16:31130400-31140400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr16:31130400-31145000	Strong transcription	Fetal Brain Female	brain
17	chr16:31130400-31153000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr16:31130600-31134000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr16:31130600-31134000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr16:31130600-31134000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr16:31130600-31134000	Strong transcription	K562	blood
22	chr16:31130600-31134200	Strong transcription	Brain Hippocampus Middle	brain
23	chr16:31130600-31134200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr16:31130600-31135600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:31130600-31135600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr16:31130600-31135600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:31130600-31135800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr16:31130600-31135800	Strong transcription	Dnd41	blood
29	chr16:31130600-31136200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr16:31130600-31136400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr16:31130600-31136600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr16:31130600-31136600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr16:31130600-31136800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:31130600-31136800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:31130600-31138600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr16:31130600-31138600	Strong transcription	Fetal Intestine Small	intestine
37	chr16:31130600-31138800	Strong transcription	Fetal Intestine Large	intestine
38	chr16:31130600-31139000	Strong transcription	Fetal Muscle Leg	muscle
39	chr16:31130600-31139600	Strong transcription	Adipose Nuclei	Adipose
40	chr16:31130600-31140600	Weak transcription	Right Atrium	heart
41	chr16:31130600-31144400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr16:31130600-31144800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr16:31130600-31144800	Strong transcription	Thymus	Thymus
44	chr16:31130600-31145000	Weak transcription	Fetal Heart	heart
45	chr16:31130600-31145200	Strong transcription	Fetal Stomach	stomach
46	chr16:31130800-31134200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr16:31130800-31135800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:31130800-31139400	Strong transcription	Primary T cells from cord blood	blood
49	chr16:31130800-31143800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr16:31130800-31144200	Strong transcription	Liver	Liver

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