Variant report

Variant	rs3764351
Chromosome Location	chr17:37824339-37824340
allele	C/T
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	YY1	chr17:37823679-37825084	K562	blood:	n/a	chr17:37823814-37823823 chr17:37823817-37823826 chr17:37824597-37824616 chr17:37824711-37824725 chr17:37824225-37824239 chr17:37824518-37824532
2	POLR2A	chr17:37823556-37825166	K562	blood:	n/a	n/a
3	POLR2A	chr17:37823100-37824994	K562	blood:	n/a	n/a
4	ZBTB7A	chr17:37823027-37825041	K562	blood:	n/a	chr17:37824004-37824012 chr17:37824015-37824026 chr17:37824298-37824305
5	RCOR1	chr17:37823151-37825237	K562	blood:	n/a	n/a
6	UBTF	chr17:37823641-37825091	K562	blood:	n/a	n/a
7	POLR2A	chr17:37819928-37825272	K562	blood:	n/a	n/a
8	MYC	chr17:37823239-37825086	K562	blood:	n/a	chr17:37824602-37824611 chr17:37823321-37823330
9	EGR1	chr17:37823605-37825268	K562	blood:	n/a	chr17:37824635-37824648 chr17:37825132-37825145 chr17:37824372-37824381 chr17:37824630-37824652 chr17:37824635-37824645 chr17:37825131-37825146 chr17:37824195-37824219
10	ZBTB7A	chr17:37822966-37824999	K562	blood:	n/a	chr17:37824004-37824012 chr17:37824015-37824026 chr17:37824298-37824305
11	ZBTB7A	chr17:37823808-37825078	ECC-1	luminal epithelium:	n/a	chr17:37824004-37824012 chr17:37824015-37824026 chr17:37824298-37824305
12	MAX	chr17:37824291-37825311	A549	lung:	n/a	chr17:37824602-37824611
13	MAZ	chr17:37822599-37825070	K562	blood:	n/a	chr17:37824602-37824611 chr17:37823321-37823330
14	MAX	chr17:37823177-37825116	K562	blood:	n/a	chr17:37824602-37824611 chr17:37823321-37823330
15	POLR2A	chr17:37823211-37825009	K562	blood:	n/a	n/a
16	ZBTB7A	chr17:37823619-37824973	ECC-1	luminal epithelium:	n/a	chr17:37824004-37824012 chr17:37824015-37824026 chr17:37824298-37824305
17	POLR2A	chr17:37822471-37825024	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37820932..37826284-chr17:37838504..37843351,7	K562	blood:
2	chr17:37775807..37781695-chr17:37822673..37828377,10	K562	blood:
3	chr17:37791520..37796368-chr17:37822308..37826994,8	K562	blood:
4	chr17:37821804..37826261-chr17:37885454..37888153,4	K562	blood:
5	chr17:37809503..37812375-chr17:37822536..37826640,4	K562	blood:
6	chr17:37702516..37704166-chr17:37823518..37825070,2	K562	blood:
7	chr17:37777756..37783081-chr17:37819129..37825010,9	K562	blood:

Variant related genes	Relation type
PNMT	TF binding region
ENSG00000141741	Chromatin interaction
ENSG00000167258	Chromatin interaction
ENSG00000131771	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000214546	Chromatin interaction
ENSG00000131748	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1053651	0.82[ASN][1000 genomes]
rs11658786	0.83[EUR][1000 genomes]
rs11869286	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877031	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs881844	0.84[EUR][1000 genomes]
rs9972882	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv908213	chr17:37807698-37839493	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv908214	chr17:37814224-37861833	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv908215	chr17:37818561-37834541	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
16	esv3377948	chr17:37823251-37825999	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3764351	PGAP3	cis	Heart Left Ventricle	GTEx
rs3764351	PGAP3	cis	Thyroid	GTEx
rs3764351	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs3764351	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37819200-37825200	Enhancers	Liver	Liver
2	chr17:37820400-37825200	Enhancers	Brain Angular Gyrus	brain
3	chr17:37821000-37824400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
4	chr17:37821200-37824600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
5	chr17:37821600-37824600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
6	chr17:37821800-37824400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr17:37821800-37825200	Active TSS	Psoas Muscle	Psoas
8	chr17:37822000-37824400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
9	chr17:37822000-37824600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:37822000-37825200	Enhancers	Lung	lung
11	chr17:37822800-37824600	Enhancers	Pancreas	Pancrea
12	chr17:37822800-37824800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:37823200-37824400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:37823200-37825200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
15	chr17:37823400-37824400	Bivalent Enhancer	Adipose Nuclei	Adipose
16	chr17:37823400-37824800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr17:37823400-37825000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:37823400-37825200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr17:37823600-37824400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr17:37823600-37824400	Active TSS	Right Atrium	heart
21	chr17:37823600-37824600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr17:37823600-37824800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr17:37823600-37824800	Active TSS	Right Ventricle	heart
24	chr17:37823600-37825000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr17:37823600-37825000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr17:37823600-37825000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr17:37823600-37825000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:37823600-37825000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:37823600-37825200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr17:37823600-37825200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr17:37823600-37825200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr17:37823800-37824400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:37823800-37824400	Active TSS	Left Ventricle	heart
34	chr17:37823800-37824400	Weak transcription	A549	lung
35	chr17:37823800-37824600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
36	chr17:37823800-37824600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr17:37823800-37824600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:37823800-37824600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr17:37823800-37824600	Active TSS	Fetal Brain Female	brain
40	chr17:37823800-37824600	Flanking Bivalent TSS/Enh	Placenta	Placenta
41	chr17:37823800-37824600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr17:37823800-37824600	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr17:37823800-37824600	Enhancers	HMEC	breast
44	chr17:37823800-37824800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:37823800-37824800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr17:37823800-37824800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:37823800-37824800	Weak transcription	Fetal Heart	heart
48	chr17:37823800-37824800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr17:37823800-37824800	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr17:37823800-37824800	Active TSS	HSMM	muscle

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