Variant report

Variant	rs3733742
Chromosome Location	chr5:68788261-68788262
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	ATF2	chr5:68788136-68789096	GM12878	blood:	n/a	n/a
2	CTCF	chr5:68788130-68788279	A549	lung:	n/a	n/a
3	HDAC2	chr5:68788203-68788854	HepG2	liver:	n/a	n/a
4	TBP	chr5:68788089-68789850	H1-hESC	embryonic stem cell:	n/a	n/a
5	TEAD4	chr5:68788063-68789621	ECC-1	luminal epithelium:	n/a	n/a
6	YY1	chr5:68788250-68788820	H1-hESC	embryonic stem cell:	n/a	chr5:68788422-68788431 chr5:68788551-68788562
7	MTA3	chr5:68787873-68790154	GM12878	blood:	n/a	n/a
8	JUND	chr5:68787994-68789754	H1-hESC	embryonic stem cell:	n/a	chr5:68789093-68789102 chr5:68789092-68789101 chr5:68789364-68789373
9	GATA3	chr5:68788246-68788787	T-47D	breast:	n/a	n/a
10	SIN3AK20	chr5:68788242-68788605	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr5:68788110-68788269	GM19238	blood:	n/a	n/a
12	POLR2A	chr5:68788225-68788793	A549	lung:	n/a	n/a
13	TCF12	chr5:68787996-68789844	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr5:68788185-68789213	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr5:68788204-68788786	A549	lung:	n/a	chr5:68788314-68788326
16	TCF12	chr5:68788007-68789836	A549	lung:	n/a	n/a
17	POLR2A	chr5:68787989-68789944	MCF-7	breast:	n/a	n/a
18	MYC	chr5:68788128-68789163	MCF-7	breast:	n/a	chr5:68788523-68788533 chr5:68788318-68788328
19	MYBL2	chr5:68787957-68788816	HepG2	liver:	n/a	n/a
20	MAX	chr5:68788135-68788781	GM12878	blood:	n/a	chr5:68788523-68788533 chr5:68788318-68788328
21	PML	chr5:68788077-68788872	MCF-7	breast:	n/a	n/a
22	NRF1	chr5:68787766-68788797	SK-N-SH	brain:	n/a	chr5:68788539-68788553 chr5:68788539-68788550 chr5:68788536-68788550
23	CTCF	chr5:68788160-68788310	Caco-2	colon:	n/a	n/a
24	TAF1	chr5:68788047-68789919	H1-hESC	embryonic stem cell:	n/a	n/a
25	NFIC	chr5:68788185-68788480	HepG2	liver:	n/a	n/a
26	SP1	chr5:68787965-68788817	A549	lung:	n/a	chr5:68788315-68788327 chr5:68788239-68788248 chr5:68788239-68788253 chr5:68788317-68788326 chr5:68788316-68788330 chr5:68788315-68788327 chr5:68788238-68788250
27	RAD21	chr5:68788146-68789045	ECC-1	luminal epithelium:	n/a	chr5:68788410-68788424 chr5:68788928-68788938 chr5:68788927-68788940
28	POLR2A	chr5:68788137-68789121	GM12878	blood:	n/a	n/a
29	MXI1	chr5:68788075-68789019	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:68787913-68789760	MCF-7	breast:	n/a	n/a
31	ZBTB7A	chr5:68787639-68789971	ECC-1	luminal epithelium:	n/a	chr5:68789087-68789101
32	MYC	chr5:68788212-68788786	MCF10A-Er-Src	breast:	n/a	chr5:68788523-68788533 chr5:68788318-68788328
33	HEY1	chr5:68788077-68788908	HepG2	liver:	n/a	chr5:68788741-68788756
34	PML	chr5:68788040-68789907	GM12878	blood:	n/a	n/a
35	MAX	chr5:68788005-68789927	ECC-1	luminal epithelium:	n/a	chr5:68788523-68788533 chr5:68788318-68788328
36	POLR2A	chr5:68788206-68788814	HepG2	liver:	n/a	n/a
37	FOXA1	chr5:68788202-68788648	T-47D	breast:	n/a	n/a
38	NFIC	chr5:68788175-68789615	GM12878	blood:	n/a	n/a
39	TAF1	chr5:68788255-68789277	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr5:68788079-68788485	MCF-7	breast:	n/a	n/a
41	POLR2A	chr5:68788253-68789866	GM12891	blood:	n/a	n/a
42	SIN3AK20	chr5:68788217-68788768	PANC-1	pancreas:	n/a	n/a
43	GABPA	chr5:68787838-68788723	MCF-7	breast:	n/a	chr5:68788539-68788553 chr5:68788539-68788550 chr5:68788536-68788550
44	POLR2A	chr5:68788154-68790010	GM18505	blood:	n/a	n/a
45	POLR2A	chr5:68788046-68789785	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr5:68788143-68788967	A549	lung:	n/a	n/a
47	ELF1	chr5:68787987-68789839	GM12878	blood:	n/a	chr5:68788422-68788431 chr5:68788423-68788435
48	TAF1	chr5:68788023-68789163	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr5:68788016-68788946	HCT-116	colon:	n/a	n/a
50	POLR2A	chr5:68788259-68788983	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68388349..68391314-chr5:68786934..68789626,2	MCF-7	breast:
2	chr5:68709515..68715463-chr5:68785927..68791978,14	MCF-7	breast:
3	chr5:68714328..68717643-chr5:68787118..68789259,3	MCF-7	breast:
4	chr5:68710929..68711657-chr5:68788195..68788888,3	MCF-7	breast:
5	chr5:68664038..68667254-chr5:68786797..68789724,5	MCF-7	breast:
6	chr5:68665412..68666024-chr5:68787946..68788690,2	MCF-7	breast:
7	chr5:68787536..68790695-chr5:68794621..68799046,5	MCF-7	breast:
8	chr5:68780984..68783227-chr5:68787002..68789520,2	MCF-7	breast:
9	chr5:68786861..68791714-chr5:68792845..68799561,13	MCF-7	breast:
10	chr5:68708231..68714128-chr5:68786986..68792913,14	MCF-7	breast:
11	chr5:68786843..68790127-chr5:68821932..68828319,7	MCF-7	breast:

Variant related genes	Relation type
OCLN	TF binding region
ENSG00000152942	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000212260	Chromatin interaction
ENSG00000249295	Chromatin interaction
ENSG00000152939	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10067619	0.85[ASN][1000 genomes]
rs28404493	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28407209	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429739	0.86[ASN][1000 genomes]
rs28489109	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28513225	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28531719	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28558979	0.84[AMR][1000 genomes]
rs28562181	0.84[AMR][1000 genomes]
rs28579732	0.88[ASN][1000 genomes]
rs28612873	0.84[AMR][1000 genomes]
rs3806856	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846487	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923832	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1023116	chr5:68744307-68867282	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1034024	chr5:68760271-69118123	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3733742	GUSBP3	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68787400-68789000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr5:68787400-68791200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:68787600-68788400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:68787600-68789800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr5:68787600-68790200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr5:68787600-68790200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:68787600-68790400	Active TSS	GM12878-XiMat	blood
8	chr5:68787600-68790600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr5:68787600-68790600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr5:68787600-68790800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:68787800-68788400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:68787800-68788400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr5:68787800-68789000	Bivalent/Poised TSS	Fetal Brain Female	brain
14	chr5:68787800-68789000	Bivalent/Poised TSS	Fetal Lung	lung
15	chr5:68787800-68789200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:68787800-68789200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:68787800-68789400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
18	chr5:68787800-68789800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr5:68787800-68789800	Active TSS	Brain Anterior Caudate	brain
20	chr5:68787800-68789800	Active TSS	Duodenum Mucosa	Duodenum
21	chr5:68787800-68789800	Active TSS	Fetal Kidney	kidney
22	chr5:68787800-68790000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:68787800-68790000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr5:68787800-68790000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:68787800-68790000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
26	chr5:68787800-68790000	Active TSS	Brain Hippocampus Middle	brain
27	chr5:68787800-68790000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
28	chr5:68787800-68790000	Bivalent/Poised TSS	Small Intestine	intestine
29	chr5:68787800-68790400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:68787800-68790600	Active TSS	Pancreas	Pancrea
31	chr5:68787800-68791400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr5:68788000-68788400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:68788000-68788400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr5:68788000-68788400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr5:68788000-68788400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:68788000-68788400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
37	chr5:68788000-68788400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
38	chr5:68788000-68788400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:68788000-68788400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr5:68788000-68788400	Bivalent/Poised TSS	Thymus	Thymus
41	chr5:68788000-68788400	Enhancers	Spleen	Spleen
42	chr5:68788000-68788600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:68788000-68788600	Bivalent Enhancer	Primary B cells from cord blood	blood
44	chr5:68788000-68788600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:68788000-68788600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
46	chr5:68788000-68788600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
47	chr5:68788000-68788600	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
48	chr5:68788000-68788600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
49	chr5:68788000-68788800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:68788000-68788800	Flanking Active TSS	HMEC	breast

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