Variant report

Variant	rs4788412
Chromosome Location	chr16:30405726-30405727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr16:30405653-30407431	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr16:30405722-30406902	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr16:30404889-30406276	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr16:30405528-30407907	H1-neurons	neurons:	n/a	n/a
5	NR2F2	chr16:30405545-30406324	K562	blood:	n/a	n/a
6	POLR2A	chr16:30405610-30407554	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr16:30405682-30407399	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr16:30405106-30408009	H1-neurons	neurons:	n/a	chr16:30406917-30406930 chr16:30406091-30406100
9	MXI1	chr16:30405086-30408046	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr16:30405403-30407473	A549	lung:	n/a	chr16:30406926-30406936
11	TAF1	chr16:30405391-30406855	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr16:30405320-30406966	SK-N-SH	brain:	n/a	n/a
13	MAX	chr16:30405596-30407549	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:30405456-30407669	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr16:30405634-30407128	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr16:30405716-30406822	IMR90	lung:	n/a	n/a
17	SIN3A	chr16:30405723-30405857	H1-hESC	embryonic stem cell:	n/a	chr16:30405781-30405790
18	POLR2A	chr16:30404861-30407531	HepG2	liver:	n/a	n/a
19	POLR2A	chr16:30405707-30407343	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr16:30405559-30407735	H1-neurons	neurons:	n/a	n/a
21	MAZ	chr16:30405531-30407619	IMR90	lung:	n/a	n/a
22	POLR2A	chr16:30405720-30406227	K562	blood:	n/a	n/a
23	POLR2A	chr16:30405577-30407460	K562	blood:	n/a	n/a
24	CBX3	chr16:30405717-30406284	K562	blood:	n/a	n/a
25	POLR2A	chr16:30405514-30407345	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr16:30405558-30407545	K562	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30374634..30377122-chr16:30405649..30407903,2	K562	blood:
2	chr16:30405548..30408419-chr16:30620470..30622922,2	MCF-7	breast:
3	chr16:30077266..30078952-chr16:30405580..30407147,2	MCF-7	breast:
4	chr16:30404931..30406633-chr16:30670446..30672250,2	MCF-7	breast:
5	chr16:30405344..30408453-chr16:30439632..30442076,3	MCF-7	breast:
6	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
7	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
8	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
9	chr16:30393486..30397071-chr16:30402673..30407150,6	MCF-7	breast:
10	chr16:30405223..30408007-chr16:30567849..30569998,3	MCF-7	breast:
11	chr16:30405261..30407569-chr16:30455597..30457105,2	MCF-7	breast:
12	chr16:30364578..30368660-chr16:30404559..30407754,8	MCF-7	breast:
13	chr16:30345604..30348863-chr16:30403977..30407853,5	MCF-7	breast:
14	chr16:30368801..30385970-chr16:30403825..30413311,30	MCF-7	breast:
15	chr16:30405726..30407812-chr16:30662378..30664163,2	K562	blood:
16	chr16:30380765..30382933-chr16:30403703..30406768,3	K562	blood:
17	chr16:30379558..30384763-chr16:30404117..30407449,5	MCF-7	breast:
18	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:

No data

Variant related genes	Relation type
ZNF48	TF binding region
ENSG00000156853	Chromatin interaction
ENSG00000270466	Chromatin interaction
ENSG00000169951	Chromatin interaction
ENSG00000183604	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000260219	Chromatin interaction
ENSG00000260869	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000156858	Chromatin interaction
ENSG00000180035	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17839551	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3766	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4076091	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56353063	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking 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	37 gene(s)	inside rSNPs	diseases
9	nsv1782	chr16:30391812-30410266	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	esv3325798	chr16:30405476-30408024	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4788412	YPEL3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30405000-30405800	Enhancers	Fetal Heart	heart
2	chr16:30405000-30407400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:30405000-30407600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr16:30405200-30406000	Flanking Active TSS	Fetal Brain Female	brain
5	chr16:30405400-30405800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr16:30405400-30405800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
7	chr16:30405400-30405800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:30405400-30405800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr16:30405400-30405800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr16:30405400-30405800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr16:30405400-30405800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr16:30405400-30405800	Enhancers	Brain Hippocampus Middle	brain
13	chr16:30405400-30405800	Enhancers	Left Ventricle	heart
14	chr16:30405400-30406000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr16:30405400-30406000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr16:30405400-30406000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr16:30405400-30406000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:30405400-30406000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:30405400-30406000	Flanking Active TSS	Brain Germinal Matrix	brain
20	chr16:30405400-30406000	Flanking Active TSS	Fetal Brain Male	brain
21	chr16:30405400-30406000	Flanking Active TSS	HSMM	muscle
22	chr16:30405400-30406200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr16:30405400-30406200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr16:30405400-30406200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr16:30405400-30406200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr16:30405400-30406200	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr16:30405400-30406200	Flanking Active TSS	Fetal Thymus	thymus
28	chr16:30405400-30406200	Flanking Active TSS	NH-A	brain
29	chr16:30405400-30406400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr16:30405400-30407600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:30405400-30407800	Active TSS	Fetal Kidney	kidney
32	chr16:30405600-30405800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr16:30405600-30405800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:30405600-30405800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
35	chr16:30405600-30405800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr16:30405600-30405800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr16:30405600-30405800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr16:30405600-30405800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr16:30405600-30405800	Enhancers	Primary hematopoietic stem cells	blood
40	chr16:30405600-30405800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr16:30405600-30405800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr16:30405600-30405800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr16:30405600-30405800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr16:30405600-30405800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr16:30405600-30405800	Enhancers	Aorta	Aorta
46	chr16:30405600-30405800	Enhancers	Brain Cingulate Gyrus	brain
47	chr16:30405600-30405800	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr16:30405600-30405800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr16:30405600-30405800	Enhancers	Colon Smooth Muscle	Colon
50	chr16:30405600-30405800	Enhancers	Gastric	stomach

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