Variant report

Variant	rs28814987
Chromosome Location	chr16:31081460-31081461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:30967328..30969546-chr16:31080736..31083156,2	K562	blood:
2	chr16:31043007..31053782-chr16:31072765..31087431,40	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103496	Chromatin interaction
ENSG00000099381	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1060506	0.95[ASN][1000 genomes]
rs10871454	0.85[ASN][1000 genomes]
rs1108431	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11150604	0.89[ASN][1000 genomes]
rs11640767	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11640957	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11642003	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11642192	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11647284	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647442	0.95[ASN][1000 genomes]
rs11862744	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11864806	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864839	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865038	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11865499	0.95[ASN][1000 genomes]
rs12445650	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12448321	0.89[ASN][1000 genomes]
rs12597511	0.93[ASN][1000 genomes]
rs12716981	0.95[ASN][1000 genomes]
rs12716982	0.95[ASN][1000 genomes]
rs12934418	0.89[ASN][1000 genomes]
rs14235	0.95[ASN][1000 genomes]
rs1549293	0.95[ASN][1000 genomes]
rs17839567	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17839568	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978485	0.95[ASN][1000 genomes]
rs1978487	0.95[ASN][1000 genomes]
rs2032915	0.95[ASN][1000 genomes]
rs2288004	0.89[ASN][1000 genomes]
rs2303222	1.00[ASN][1000 genomes]
rs2303223	0.98[ASN][1000 genomes]
rs2359612	1.00[ASN][1000 genomes]
rs2855475	0.95[ASN][1000 genomes]
rs28725459	0.91[ASN][1000 genomes]
rs2884738	0.95[ASN][1000 genomes]
rs34649473	0.85[ASN][1000 genomes]
rs35351013	0.93[ASN][1000 genomes]
rs35468353	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35713203	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35961830	0.83[EUR][1000 genomes]
rs3751855	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4468641	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4527034	0.95[ASN][1000 genomes]
rs4889526	0.85[EUR][1000 genomes]
rs4889530	0.87[ASN][1000 genomes]
rs4889609	0.85[EUR][1000 genomes]
rs4889619	0.84[ASN][1000 genomes]
rs4889620	0.95[ASN][1000 genomes]
rs55766044	0.95[ASN][1000 genomes]
rs55979739	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56284083	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56314408	0.95[ASN][1000 genomes]
rs56813533	0.93[ASN][1000 genomes]
rs57434408	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57576577	0.83[EUR][1000 genomes]
rs58726213	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59061704	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59735493	0.95[ASN][1000 genomes]
rs60996860	0.91[ASN][1000 genomes]
rs61162043	1.00[ASN][1000 genomes]
rs61320757	0.95[ASN][1000 genomes]
rs6565217	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187995	0.93[ASN][1000 genomes]
rs7196161	1.00[ASN][1000 genomes]
rs7196726	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197717	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199949	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732172	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs732173	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73530203	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs749670	1.00[ASN][1000 genomes]
rs749671	1.00[ASN][1000 genomes]
rs749767	0.95[ASN][1000 genomes]
rs7500176	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs750952	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047803	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050894	1.00[ASN][1000 genomes]
rs8056842	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8061047	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs881929	1.00[ASN][1000 genomes]
rs889548	0.95[ASN][1000 genomes]
rs889555	0.95[ASN][1000 genomes]
rs9673641	0.82[EUR][1000 genomes]
rs9923231	1.00[ASN][1000 genomes]
rs9925964	0.95[ASN][1000 genomes]
rs9929899	0.86[ASN][1000 genomes]
rs9934438	1.00[ASN][1000 genomes]
rs9936329	0.95[ASN][1000 genomes]
rs9939417	0.89[ASN][1000 genomes]
rs9939558	0.89[ASN][1000 genomes]
rs9972727	0.95[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	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28814987	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs28814987	RP11-196G11.2	cis	Esophagus Muscularis	GTEx
rs28814987	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs28814987	STX4	Cis_1M	lymphoblastoid	RTeQTL
rs28814987	STX1B	cis	Thyroid	GTEx
rs28814987	RP11-196G11.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31046000-31083200	Weak transcription	Right Atrium	heart
2	chr16:31051400-31083000	Weak transcription	Fetal Lung	lung
3	chr16:31052000-31083400	Weak transcription	Primary B cells from cord blood	blood
4	chr16:31054000-31083200	Weak transcription	Fetal Kidney	kidney
5	chr16:31070400-31082600	Weak transcription	Fetal Brain Male	brain
6	chr16:31073600-31082800	Weak transcription	HepG2	liver
7	chr16:31073600-31083000	Weak transcription	Small Intestine	intestine
8	chr16:31073600-31083200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr16:31073600-31083200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:31073600-31083200	Weak transcription	Brain Substantia Nigra	brain
11	chr16:31073800-31083400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr16:31075400-31084000	Weak transcription	Ovary	ovary
13	chr16:31075600-31082800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr16:31075600-31083000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr16:31075600-31083000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr16:31075600-31083000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr16:31075600-31083000	Weak transcription	Brain Angular Gyrus	brain
18	chr16:31075600-31083000	Weak transcription	Brain Anterior Caudate	brain
19	chr16:31075600-31083000	Weak transcription	Brain Hippocampus Middle	brain
20	chr16:31075600-31083000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr16:31075600-31083200	Weak transcription	Liver	Liver
22	chr16:31075600-31083400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:31075600-31083600	Weak transcription	Gastric	stomach
24	chr16:31075600-31083800	Weak transcription	Aorta	Aorta
25	chr16:31075800-31082600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr16:31075800-31082800	Weak transcription	Fetal Brain Female	brain
27	chr16:31075800-31083000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr16:31075800-31083000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr16:31075800-31083000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr16:31075800-31083000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr16:31075800-31083000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr16:31075800-31083200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr16:31075800-31083400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr16:31075800-31083400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr16:31075800-31083400	Weak transcription	Fetal Intestine Large	intestine
36	chr16:31076000-31082800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr16:31076200-31082800	Weak transcription	Thymus	Thymus
38	chr16:31076200-31083000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr16:31076400-31083000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:31076400-31083000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr16:31076400-31083200	Weak transcription	Fetal Intestine Small	intestine
42	chr16:31076600-31082800	Weak transcription	K562	blood
43	chr16:31076600-31083000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr16:31076600-31083200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr16:31076800-31082800	Weak transcription	Adipose Nuclei	Adipose
46	chr16:31076800-31082800	Weak transcription	Hela-S3	cervix
47	chr16:31076800-31082800	Weak transcription	HUVEC	blood vessel
48	chr16:31076800-31083000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr16:31076800-31083000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr16:31076800-31083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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