Variant report

Variant	rs4147595
Chromosome Location	chr1:165601215-165601216
allele	C/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	CTCF	chr1:165601080-165601230	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr1:165601080-165601230	GM12874	blood:	n/a	n/a
3	CTCF	chr1:165601140-165601290	HPF	lung:	n/a	n/a
4	JUND	chr1:165599729-165601691	K562	blood:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165601292-165601302
5	CTCF	chr1:165601140-165601290	AG04450	lung:	n/a	n/a
6	CTCF	chr1:165601170-165601328	MCF-7	breast:	n/a	n/a
7	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
8	CTCF	chr1:165601160-165601310	HRE	kidney:	n/a	n/a
9	POLR2A	chr1:165601086-165601379	HCT-116	colon:	n/a	n/a
10	RAD21	chr1:165600994-165601375	SK-N-SH_RA	brain:	n/a	n/a
11	TAF1	chr1:165601052-165601445	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr1:165601172-165601237	H1-hESC	embryonic stem cell:	n/a	n/a
13	BRCA1	chr1:165601074-165601651	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr1:165601100-165601250	GM12871	blood:	n/a	n/a
15	POLR2A	chr1:165601179-165601289	HUVEC	blood vessel:	n/a	n/a
16	FOS	chr1:165601090-165601830	MCF10A-Er-Src	breast:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165601291-165601302 chr1:165601292-165601302 chr1:165601697-165601708
17	CTCF	chr1:165601200-165601350	HL-60	blood:	n/a	n/a
18	POLR2A	chr1:165600822-165601584	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr1:165601160-165601310	A549	lung:	n/a	n/a
20	EBF1	chr1:165601055-165601424	GM12878	blood:	n/a	n/a
21	ZNF263	chr1:165599801-165601616	HEK293-T-REx	kidney:	n/a	n/a
22	ZNF143	chr1:165599863-165601392	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAZ	chr1:165599482-165601556	K562	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
24	CEBPB	chr1:165600853-165601649	IMR90	lung:	n/a	n/a
25	CTCF	chr1:165601160-165601310	AoAF	blood vessel:	n/a	n/a
26	CTCF	chr1:165601080-165601230	HCFaa	heart:	n/a	n/a
27	RCOR1	chr1:165599665-165601710	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:165600944-165601416	SK-N-SH	brain:	n/a	n/a
29	CCNT2	chr1:165599835-165601392	K562	blood:	n/a	n/a
30	MAX	chr1:165601066-165601555	K562	blood:	n/a	n/a
31	MYC	chr1:165601135-165601729	MCF10A-Er-Src	breast:	n/a	n/a
32	NFIC	chr1:165601030-165601526	GM12878	blood:	n/a	n/a
33	MAZ	chr1:165599566-165601374	GM12878	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
34	CTCF	chr1:165600981-165601412	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:165599494-165601603	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:165600837-165601565	Hela-S3	cervix:	n/a	n/a
37	FOXM1	chr1:165600947-165601470	GM12878	blood:	n/a	n/a
38	MXI1	chr1:165598861-165601697	SK-N-SH	brain:	n/a	n/a
39	FOS	chr1:165601025-165601662	MCF10A-Er-Src	breast:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165601291-165601302 chr1:165601292-165601302
40	MYC	chr1:165599562-165601677	Hela-S3	cervix:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
41	TFAP2C	chr1:165599700-165601723	Hela-S3	cervix:	n/a	chr1:165600451-165600466 chr1:165601477-165601492 chr1:165601459-165601474
42	ELF1	chr1:165601182-165601802	MCF-7	breast:	n/a	n/a
43	MAX	chr1:165600824-165601569	SK-N-SH	brain:	n/a	n/a
44	MXI1	chr1:165599516-165601730	IMR90	lung:	n/a	n/a
45	CTCF	chr1:165601160-165601310	NB4	blood:	n/a	n/a
46	POLR2A	chr1:165599430-165601655	K562	blood:	n/a	n/a
47	CTCF	chr1:165601191-165601290	K562	blood:	n/a	n/a
48	MAFK	chr1:165600976-165601555	K562	blood:	n/a	n/a
49	JUN	chr1:165599850-165601825	K562	blood:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165601292-165601302 chr1:165601697-165601708
50	CTCF	chr1:165601140-165601290	RPTEC	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:165600483..165602839-chr1:165648702..165651325,2	K562	blood:
2	chr1:165598732..165600312-chr1:165601060..165603402,2	MCF-7	breast:
3	chr1:165599775..165601444-chr1:165795750..165798255,2	K562	blood:
4	chr1:165599643..165601355-chr1:165666069..165669053,3	MCF-7	breast:
5	chr1:165597575..165602245-chr1:165617678..165620274,4	K562	blood:
6	chr1:165599737..165602284-chr1:165666440..165669733,4	K562	blood:
7	chr1:165598109..165601268-chr1:165795469..165798298,3	MCF-7	breast:
8	chr1:165598557..165602218-chr1:165613054..165616011,3	K562	blood:
9	chr1:165600033..165602839-chr1:165649825..165652028,2	K562	blood:
10	chr1:165600029..165602046-chr1:165667210..165669353,5	K562	blood:

Variant related genes	Relation type
MGST3	TF binding region
ENSG00000215838	Chromatin interaction
ENSG00000143149	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10733045	0.81[ASN][1000 genomes]
rs10737515	0.87[ASN][1000 genomes]
rs10800118	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10800120	0.87[CHB][hapmap]
rs10918223	0.87[ASN][1000 genomes]
rs12040685	0.88[ASN][1000 genomes]
rs2348733	1.00[CEU][hapmap];0.88[CHB][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4147591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147592	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4147593	0.89[ASN][1000 genomes]
rs4147594	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147596	0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147597	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs4147598	0.87[CHB][hapmap]
rs4147600	0.87[CHB][hapmap]
rs6426925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6426926	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs6694924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4147595	MGST3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165599000-165601400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:165599000-165601400	Active TSS	Brain Angular Gyrus	brain
3	chr1:165599000-165601600	Active TSS	A549	lung
4	chr1:165599000-165601800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:165599000-165602000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:165599000-165602000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:165599000-165602000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:165599000-165602000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:165599200-165601400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:165599200-165601400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:165599200-165601400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:165599200-165601400	Active TSS	Brain Anterior Caudate	brain
13	chr1:165599200-165601400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:165599200-165601400	Active TSS	Osteobl	bone
15	chr1:165599200-165601600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:165599200-165601600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:165599200-165601600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:165599200-165601800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:165599200-165601800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:165599200-165602200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:165599200-165602200	Active TSS	NHDF-Ad	bronchial
22	chr1:165599200-165602200	Active TSS	NHLF	lung
23	chr1:165599200-165603400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:165599400-165601400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:165599400-165601400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:165599400-165601400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:165599400-165601400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:165599400-165601400	Active TSS	Colon Smooth Muscle	Colon
29	chr1:165599400-165601400	Active TSS	Placenta	Placenta
30	chr1:165599400-165601400	Active TSS	Pancreas	Pancrea
31	chr1:165599400-165601400	Active TSS	HSMMtube	muscle
32	chr1:165599400-165601600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:165599400-165601600	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr1:165599400-165601600	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:165599400-165601600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:165599400-165601600	Active TSS	Stomach Mucosa	stomach
37	chr1:165599400-165601800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:165599400-165601800	Active TSS	H1 Cell Line	embryonic stem cell
39	chr1:165599400-165601800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:165599400-165601800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:165599400-165601800	Active TSS	Fetal Kidney	kidney
42	chr1:165599400-165602000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:165599400-165602000	Active TSS	Colonic Mucosa	Colon
44	chr1:165599400-165602200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:165599400-165602400	Active TSS	Ovary	ovary
46	chr1:165599400-165602400	Active TSS	Stomach Smooth Muscle	stomach
47	chr1:165599400-165602600	Active TSS	Right Ventricle	heart
48	chr1:165599400-165602800	Active TSS	Left Ventricle	heart
49	chr1:165599400-165602800	Active TSS	Psoas Muscle	Psoas
50	chr1:165599400-165603000	Active TSS	Aorta	Aorta

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