Variant report

Variant	rs56353063
Chromosome Location	chr16:30361995-30361996
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:99)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:99 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr16:30361663-30362412	GM12878	blood:	n/a	n/a
2	NFYB	chr16:30361932-30362188	GM12878	blood:	n/a	n/a
3	RELA	chr16:30361815-30362263	GM19099	blood:	n/a	n/a
4	POLR2A	chr16:30361813-30362041	A549	lung:	n/a	n/a
5	TBP	chr16:30361888-30362160	GM12878	blood:	n/a	n/a
6	BCL11A	chr16:30361786-30362224	GM12878	blood:	n/a	n/a
7	POLR2A	chr16:30360497-30362289	K562	blood:	n/a	n/a
8	ZNF143	chr16:30361876-30362082	GM12878	blood:	n/a	n/a
9	RUNX3	chr16:30360896-30362575	GM12878	blood:	n/a	n/a
10	BCLAF1	chr16:30361656-30362327	GM12878	blood:	n/a	n/a
11	POLR2A	chr16:30361701-30362129	U87	brain:	n/a	n/a
12	IKZF1	chr16:30361699-30362333	GM12878	blood:	n/a	n/a
13	SP1	chr16:30361778-30362241	GM12878	blood:	n/a	n/a
14	ATF2	chr16:30361646-30362301	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:30361877-30362145	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:30361755-30362234	GM12891	blood:	n/a	n/a
17	STAT1	chr16:30361946-30362138	GM12878	blood:	n/a	n/a
18	WRNIP1	chr16:30361840-30362155	GM12878	blood:	n/a	n/a
19	NFATC1	chr16:30361715-30362306	GM12878	blood:	n/a	n/a
20	STAT3	chr16:30361893-30362202	GM12878	blood:	n/a	n/a
21	POU2F2	chr16:30361774-30362304	GM12891	blood:	n/a	n/a
22	POU2F2	chr16:30361787-30362169	GM12878	blood:	n/a	n/a
23	POLR2A	chr16:30361849-30362263	GM12878	blood:	n/a	n/a
24	EP300	chr16:30361716-30362273	GM12878	blood:	n/a	n/a
25	CEBPB	chr16:30361662-30362397	GM12878	blood:	n/a	n/a
26	POU2F2	chr16:30361765-30362260	GM12891	blood:	n/a	n/a
27	MAX	chr16:30361817-30362138	GM12878	blood:	n/a	n/a
28	ZNF384	chr16:30360882-30362175	GM12878	blood:	n/a	n/a
29	MTA3	chr16:30361446-30362262	GM12878	blood:	n/a	n/a
30	FOSL2	chr16:30361782-30362614	HepG2	liver:	n/a	n/a
31	POLR2A	chr16:30361852-30362726	K562	blood:	n/a	n/a
32	ATF2	chr16:30361781-30362285	GM12878	blood:	n/a	n/a
33	POLR2A	chr16:30361648-30362670	H1-hESC	embryonic stem cell:	n/a	n/a
34	PAX5	chr16:30361844-30362242	GM12891	blood:	n/a	n/a
35	POLR2A	chr16:30361795-30362071	HUVEC	blood vessel:	n/a	n/a
36	ZEB1	chr16:30361628-30362075	GM12878	blood:	n/a	chr16:30361899-30361907
37	SP1	chr16:30361728-30362282	GM12878	blood:	n/a	n/a
38	NFIC	chr16:30361689-30362349	GM12878	blood:	n/a	n/a
39	PML	chr16:30361538-30362375	GM12878	blood:	n/a	n/a
40	MEF2A	chr16:30361708-30362342	GM12878	blood:	n/a	n/a
41	CHD2	chr16:30361891-30362193	GM12878	blood:	n/a	n/a
42	POLR2A	chr16:30361783-30362083	K562	blood:	n/a	n/a
43	POLR2A	chr16:30360110-30369693	HepG2	liver:	n/a	n/a
44	SMC3	chr16:30361877-30362146	GM12878	blood:	n/a	n/a
45	POLR2A	chr16:30361469-30362080	MCF-7	breast:	n/a	n/a
46	POLR2A	chr16:30361447-30362511	SK-N-SH	brain:	n/a	n/a
47	MAZ	chr16:30361814-30362197	GM12878	blood:	n/a	n/a
48	POLR2A	chr16:30361697-30362114	K562	blood:	n/a	n/a
49	YY1	chr16:30361783-30362074	GM12878	blood:	n/a	n/a
50	FOXM1	chr16:30361496-30362286	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30352018..30354393-chr16:30361515..30363064,2	K562	blood:
2	chr16:30352836..30354996-chr16:30361711..30364215,3	MCF-7	breast:
3	chr16:30352018..30354581-chr16:30361515..30364164,2	K562	blood:
4	chr16:30352266..30354018-chr16:30359193..30362629,3	MCF-7	breast:
5	chr16:30347434..30350400-chr16:30361325..30364299,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260219	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17839551	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3766	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4076091	0.85[AMR][1000 genomes]
rs4788412	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061165	chr16:29657389-30363743	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
4	esv2758420	chr16:30073955-30383280	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	esv2758642	chr16:30073955-30383280	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56353063	YPEL3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30347400-30362000	Weak transcription	Brain Substantia Nigra	brain
2	chr16:30347400-30362200	Weak transcription	Aorta	Aorta
3	chr16:30347400-30363400	Weak transcription	Brain Angular Gyrus	brain
4	chr16:30347600-30362000	Weak transcription	Colonic Mucosa	Colon
5	chr16:30347600-30362200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr16:30347600-30363000	Weak transcription	Psoas Muscle	Psoas
7	chr16:30349200-30362000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr16:30352400-30362000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr16:30358800-30362200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr16:30359000-30362000	Weak transcription	HSMMtube	muscle
11	chr16:30359000-30363000	Weak transcription	Stomach Mucosa	stomach
12	chr16:30359200-30362200	Weak transcription	Small Intestine	intestine
13	chr16:30359400-30362000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr16:30359400-30362000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr16:30359400-30362200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr16:30359400-30362200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr16:30359400-30362800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr16:30359800-30362000	Enhancers	Primary B cells from peripheral blood	blood
19	chr16:30359800-30362800	Weak transcription	Hela-S3	cervix
20	chr16:30360000-30362200	Weak transcription	Ovary	ovary
21	chr16:30360000-30363000	Weak transcription	Fetal Heart	heart
22	chr16:30360000-30363800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr16:30360200-30362600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr16:30360200-30365600	Weak transcription	Fetal Kidney	kidney
25	chr16:30360400-30365000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr16:30360600-30363400	Strong transcription	Fetal Stomach	stomach
27	chr16:30360600-30364000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr16:30360600-30364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr16:30360600-30365200	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr16:30360600-30365200	Strong transcription	NHEK	skin
31	chr16:30360800-30362600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr16:30360800-30365000	Strong transcription	Fetal Thymus	thymus
33	chr16:30360800-30365200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr16:30361000-30362200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:30361000-30362400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr16:30361000-30363000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr16:30361000-30363000	Strong transcription	Brain Hippocampus Middle	brain
38	chr16:30361000-30363000	Strong transcription	Fetal Muscle Leg	muscle
39	chr16:30361000-30363000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr16:30361000-30363200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr16:30361000-30363400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:30361000-30363400	Strong transcription	Dnd41	blood
43	chr16:30361000-30363400	Strong transcription	HMEC	breast
44	chr16:30361000-30364400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr16:30361000-30364400	Strong transcription	Placenta	Placenta
46	chr16:30361000-30364600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr16:30361000-30364600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr16:30361000-30364600	Strong transcription	K562	blood
49	chr16:30361000-30365200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr16:30361000-30365200	Strong transcription	Primary monocytes fromperipheralblood	blood

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