Variant report

Variant	rs4147593
Chromosome Location	chr1:165600267-165600268
allele	A/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	FOSL2	chr1:165599753-165600413	A549	lung:	n/a	n/a
2	STAT5A	chr1:165599668-165600892	GM12878	blood:	n/a	n/a
3	CEBPB	chr1:165599821-165600630	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:165599688-165600718	GM12878	blood:	n/a	n/a
5	JUND	chr1:165599729-165601691	K562	blood:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165601292-165601302
6	CEBPB	chr1:165599766-165600387	ECC-1	luminal epithelium:	n/a	n/a
7	YY1	chr1:165599873-165600668	SK-N-SH_RA	brain:	n/a	n/a
8	ZEB1	chr1:165600159-165600802	GM12878	blood:	n/a	chr1:165600524-165600537
9	GTF2F1	chr1:165599746-165600632	H1-hESC	embryonic stem cell:	n/a	n/a
10	ELF1	chr1:165599888-165600423	A549	lung:	n/a	n/a
11	E2F6	chr1:165599491-165600711	H1-hESC	embryonic stem cell:	n/a	chr1:165599538-165599550 chr1:165600079-165600086 chr1:165599560-165599574 chr1:165600079-165600086 chr1:165600083-165600092 chr1:165599680-165599689 chr1:165600079-165600086 chr1:165600425-165600435
12	KAT2A	chr1:165599847-165600360	Hela-S3	cervix:	n/a	n/a
13	BHLHE40	chr1:165599454-165600628	HepG2	liver:	n/a	chr1:165600559-165600575
14	FOS	chr1:165599857-165601558	HUVEC	blood vessel:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165601291-165601302 chr1:165601292-165601302
15	TEAD4	chr1:165599800-165600350	K562	blood:	n/a	n/a
16	ELF1	chr1:165599790-165600603	K562	blood:	n/a	chr1:165600419-165600431
17	EP300	chr1:165599877-165600353	HepG2	liver:	n/a	n/a
18	MAX	chr1:165599339-165600843	ECC-1	luminal epithelium:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
19	EGR1	chr1:165599793-165600558	K562	blood:	n/a	chr1:165600025-165600034 chr1:165600023-165600037 chr1:165600083-165600092 chr1:165600025-165600036 chr1:165600024-165600037 chr1:165600021-165600035 chr1:165600025-165600036 chr1:165600082-165600091 chr1:165600024-165600037 chr1:165600024-165600037 chr1:165600019-165600041 chr1:165600024-165600037 chr1:165600025-165600035 chr1:165600025-165600035
20	SP1	chr1:165599680-165600723	A549	lung:	n/a	chr1:165600421-165600430 chr1:165599713-165599722 chr1:165600421-165600431 chr1:165599878-165599888 chr1:165599712-165599724 chr1:165600451-165600460 chr1:165599690-165599704 chr1:165600422-165600431 chr1:165600450-165600462 chr1:165600394-165600406 chr1:165600420-165600432 chr1:165600451-165600460 chr1:165600395-165600405 chr1:165600028-165600038 chr1:165600422-165600431 chr1:165600420-165600432 chr1:165600395-165600405 chr1:165600452-165600461 chr1:165599680-165599689 chr1:165600394-165600406 chr1:165600450-165600462 chr1:165599713-165599722 chr1:165599712-165599724 chr1:165600451-165600461 chr1:165599714-165599723
21	E2F4	chr1:165599850-165600633	K562	blood:	n/a	chr1:165600079-165600086 chr1:165600079-165600086 chr1:165600083-165600092 chr1:165600079-165600086 chr1:165600425-165600435
22	SP4	chr1:165599682-165600796	H1-hESC	embryonic stem cell:	n/a	chr1:165600392-165600408 chr1:165600418-165600434 chr1:165599875-165599891 chr1:165599873-165599889 chr1:165600390-165600406
23	YY1	chr1:165599928-165600711	GM12892	blood:	n/a	n/a
24	ZNF263	chr1:165599801-165601616	HEK293-T-REx	kidney:	n/a	n/a
25	ZNF143	chr1:165599863-165601392	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr1:165599689-165600633	MCF-7	breast:	n/a	chr1:165600026-165600035
27	TAF1	chr1:165599759-165600824	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr1:165599684-165600782	GM12892	blood:	n/a	n/a
29	MAZ	chr1:165599482-165601556	K562	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
30	CREB1	chr1:165599708-165600738	K562	blood:	n/a	n/a
31	POLR2A	chr1:165598911-165600810	SK-N-MC	brain:	n/a	n/a
32	THAP1	chr1:165599793-165600587	K562	blood:	n/a	n/a
33	MAX	chr1:165599480-165600820	ECC-1	luminal epithelium:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
34	BCLAF1	chr1:165599732-165600705	GM12878	blood:	n/a	chr1:165600663-165600670
35	WRNIP1	chr1:165599857-165600409	GM12878	blood:	n/a	n/a
36	ELF1	chr1:165599889-165600373	MCF-7	breast:	n/a	n/a
37	MXI1	chr1:165599743-165600914	H1-hESC	embryonic stem cell:	n/a	n/a
38	BHLHE40	chr1:165599622-165600640	GM12878	blood:	n/a	chr1:165600559-165600575
39	RCOR1	chr1:165599665-165601710	Hela-S3	cervix:	n/a	n/a
40	MAX	chr1:165599354-165600852	HepG2	liver:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
41	CCNT2	chr1:165599835-165601392	K562	blood:	n/a	n/a
42	EP300	chr1:165599917-165600629	GM12878	blood:	n/a	n/a
43	TCF7L2	chr1:165599391-165600682	HCT-116	colon:	n/a	chr1:165599758-165599768 chr1:165599756-165599772 chr1:165599756-165599772 chr1:165599759-165599768
44	MAX	chr1:165599708-165600499	A549	lung:	n/a	chr1:165600026-165600035
45	BACH1	chr1:165599762-165600994	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAZ	chr1:165599566-165601374	GM12878	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
47	POLR2A	chr1:165599906-165600779	ProgFib	skin:	n/a	n/a
48	MAZ	chr1:165599944-165600904	HepG2	liver:	n/a	chr1:165600026-165600035
49	BCL3	chr1:165599815-165600742	A549	lung:	n/a	chr1:165600663-165600670
50	MAX	chr1:165599368-165600823	K562	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691

No.	Distal block	Cell Line	Cell type
1	chr1:165598732..165600312-chr1:165601060..165603402,2	MCF-7	breast:
2	chr1:165599477..165601110-chr1:165618354..165620160,2	K562	blood:
3	chr1:165598675..165601057-chr1:165860826..165863471,2	K562	blood:
4	chr1:165599982..165600842-chr19:48949009..48949600,2	NB4	blood:
5	chr1:165599775..165601444-chr1:165795750..165798255,2	K562	blood:
6	chr1:165599942..165600511-chr5:40835018..40835753,2	Hela-S3	cervix:
7	chr1:165599824..165600496-chr7:155089620..155090555,2	NB4	blood:
8	chr1:165599643..165601355-chr1:165666069..165669053,3	MCF-7	breast:
9	chr1:165597575..165602245-chr1:165617678..165620274,4	K562	blood:
10	chr1:165599737..165602284-chr1:165666440..165669733,4	K562	blood:
11	chr1:165598109..165601268-chr1:165795469..165798298,3	MCF-7	breast:
12	chr1:165598557..165602218-chr1:165613054..165616011,3	K562	blood:
13	chr1:165600033..165602839-chr1:165649825..165652028,2	K562	blood:
14	chr1:165599820..165600395-chr1:165738023..165738865,2	Hela-S3	cervix:
15	chr1:165600104..165600920-chr2:85132456..85133129,2	Hela-S3	cervix:
16	chr1:165600029..165602046-chr1:165667210..165669353,5	K562	blood:

Variant related genes	Relation type
MGST3	TF binding region
ENSG00000143198	Chromatin interaction
ENSG00000143149	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000034510	Chromatin interaction
ENSG00000186480	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000105447	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000224358	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10733045	0.91[ASN][1000 genomes]
rs10737515	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10800118	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918223	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040685	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147591	0.88[ASN][1000 genomes]
rs4147592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4147594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147595	0.89[ASN][1000 genomes]
rs4147596	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147599	0.80[ASN][1000 genomes]
rs6694924	0.87[ASN][1000 genomes]
rs9333413	0.80[AFR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4147593	MGST3	Cis_1M	lymphoblastoid	RTeQTL
rs4147593	MGST3	cis	Esophagus Mucosa	GTEx
rs4147593	MGST3	cis	multi-tissue	Pritchard
rs4147593	MGST3	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165598400-165600800	Active TSS	Fetal Brain Male	brain
2	chr1:165599000-165601400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:165599000-165601400	Active TSS	Brain Angular Gyrus	brain
4	chr1:165599000-165601600	Active TSS	A549	lung
5	chr1:165599000-165601800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:165599000-165602000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:165599000-165602000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:165599000-165602000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:165599000-165602000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:165599200-165601200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:165599200-165601400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:165599200-165601400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:165599200-165601400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:165599200-165601400	Active TSS	Brain Anterior Caudate	brain
15	chr1:165599200-165601400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:165599200-165601400	Active TSS	Osteobl	bone
17	chr1:165599200-165601600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:165599200-165601600	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:165599200-165601600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:165599200-165601800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:165599200-165601800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:165599200-165602200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:165599200-165602200	Active TSS	NHDF-Ad	bronchial
24	chr1:165599200-165602200	Active TSS	NHLF	lung
25	chr1:165599200-165603400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:165599400-165600400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr1:165599400-165600400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:165599400-165600800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr1:165599400-165601400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:165599400-165601400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:165599400-165601400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:165599400-165601400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:165599400-165601400	Active TSS	Colon Smooth Muscle	Colon
34	chr1:165599400-165601400	Active TSS	Placenta	Placenta
35	chr1:165599400-165601400	Active TSS	Pancreas	Pancrea
36	chr1:165599400-165601400	Active TSS	HSMMtube	muscle
37	chr1:165599400-165601600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:165599400-165601600	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:165599400-165601600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:165599400-165601600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:165599400-165601600	Active TSS	Stomach Mucosa	stomach
42	chr1:165599400-165601800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr1:165599400-165601800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr1:165599400-165601800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:165599400-165601800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:165599400-165601800	Active TSS	Fetal Kidney	kidney
47	chr1:165599400-165602000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:165599400-165602000	Active TSS	Colonic Mucosa	Colon
49	chr1:165599400-165602200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:165599400-165602400	Active TSS	Ovary	ovary

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