Variant report

Variant	rs9333372
Chromosome Location	chr1:165600766-165600767
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	STAT5A	chr1:165599668-165600892	GM12878	blood:	n/a	n/a
2	JUND	chr1:165599729-165601691	K562	blood:	n/a	chr1:165601294-165601301 chr1:165601292-165601301 chr1:165601130-165601140 chr1:165601292-165601302 chr1:165601292-165601302
3	ZEB1	chr1:165600159-165600802	GM12878	blood:	n/a	chr1:165600524-165600537
4	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
5	MAX	chr1:165599339-165600843	ECC-1	luminal epithelium:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
6	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
7	ZNF263	chr1:165599801-165601616	HEK293-T-REx	kidney:	n/a	n/a
8	ZNF143	chr1:165599863-165601392	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr1:165599759-165600824	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr1:165599684-165600782	GM12892	blood:	n/a	n/a
11	MAZ	chr1:165599482-165601556	K562	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
12	POLR2A	chr1:165598911-165600810	SK-N-MC	brain:	n/a	n/a
13	MAX	chr1:165599480-165600820	ECC-1	luminal epithelium:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
14	MXI1	chr1:165599743-165600914	H1-hESC	embryonic stem cell:	n/a	n/a
15	RCOR1	chr1:165599665-165601710	Hela-S3	cervix:	n/a	n/a
16	MAX	chr1:165599354-165600852	HepG2	liver:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
17	CCNT2	chr1:165599835-165601392	K562	blood:	n/a	n/a
18	BACH1	chr1:165599762-165600994	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAZ	chr1:165599566-165601374	GM12878	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
20	POLR2A	chr1:165599906-165600779	ProgFib	skin:	n/a	n/a
21	MAZ	chr1:165599944-165600904	HepG2	liver:	n/a	chr1:165600026-165600035
22	MAX	chr1:165599368-165600823	K562	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
23	POLR2A	chr1:165599611-165600783	K562	blood:	n/a	n/a
24	POLR2A	chr1:165599494-165601603	Hela-S3	cervix:	n/a	n/a
25	MXI1	chr1:165598861-165601697	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr1:165600680-165600830	HEEpiC	esophagus:	n/a	n/a
27	POLR2A	chr1:165599701-165600822	HUVEC	blood vessel:	n/a	n/a
28	CHD2	chr1:165599866-165600864	K562	blood:	n/a	n/a
29	MYC	chr1:165599562-165601677	Hela-S3	cervix:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
30	TFAP2C	chr1:165599700-165601723	Hela-S3	cervix:	n/a	chr1:165600451-165600466 chr1:165601477-165601492 chr1:165601459-165601474
31	GATA2	chr1:165600055-165601028	HUVEC	blood vessel:	n/a	chr1:165600662-165600671 chr1:165600660-165600673 chr1:165600821-165600831 chr1:165600660-165600672 chr1:165600658-165600674
32	MXI1	chr1:165599516-165601730	IMR90	lung:	n/a	n/a
33	POLR2A	chr1:165599662-165600830	U87	brain:	n/a	n/a
34	MYC	chr1:165599488-165600806	K562	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
35	POLR2A	chr1:165599730-165600901	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:165599430-165601655	K562	blood:	n/a	n/a
37	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
38	POLR2A	chr1:165599530-165600769	MCF-7	breast:	n/a	n/a
39	TCF12	chr1:165599604-165600800	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:165599766-165600766	K562	blood:	n/a	n/a
41	EP300	chr1:165599817-165601651	K562	blood:	n/a	chr1:165601292-165601301
42	ZNF384	chr1:165599310-165600821	K562	blood:	n/a	n/a
43	ZMIZ1	chr1:165599755-165601574	K562	blood:	n/a	n/a
44	MAZ	chr1:165599616-165601608	Hela-S3	cervix:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
45	POLR2A	chr1:165599846-165601628	IMR90	lung:	n/a	n/a
46	MAX	chr1:165599640-165600963	GM12878	blood:	n/a	chr1:165600026-165600035 chr1:165599681-165599691
47	TBL1XR1	chr1:165599814-165600923	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:165599781-165601666	PBDE	blood:	n/a	n/a
49	ELF1	chr1:165600720-165601138	K562	blood:	n/a	chr1:165600840-165600852
50	CTCF	chr1:165600620-165600770	AoAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:165599477..165601110-chr1:165618354..165620160,2	K562	blood:
2	chr1:165598675..165601057-chr1:165860826..165863471,2	K562	blood:
3	chr1:165599982..165600842-chr19:48949009..48949600,2	NB4	blood:
4	chr1:165600483..165602839-chr1:165648702..165651325,2	K562	blood:
5	chr1:165599775..165601444-chr1:165795750..165798255,2	K562	blood:
6	chr1:165600432..165601058-chr18:71815301..71816132,2	HCT-116	colon:
7	chr1:165599643..165601355-chr1:165666069..165669053,3	MCF-7	breast:
8	chr1:165597575..165602245-chr1:165617678..165620274,4	K562	blood:
9	chr1:165599737..165602284-chr1:165666440..165669733,4	K562	blood:
10	chr1:165598109..165601268-chr1:165795469..165798298,3	MCF-7	breast:
11	chr1:165600481..165601208-chr8:17013484..17014169,2	Hela-S3	cervix:
12	chr1:165598557..165602218-chr1:165613054..165616011,3	K562	blood:
13	chr1:165600033..165602839-chr1:165649825..165652028,2	K562	blood:
14	chr1:165600104..165600920-chr2:85132456..85133129,2	Hela-S3	cervix:
15	chr1:165600029..165602046-chr1:165667210..165669353,5	K562	blood:

Variant related genes	Relation type
MGST3	TF binding region
ENSG00000143149	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000105447	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000075336	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000104219	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000034510	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16848502	0.89[CEU][hapmap];0.86[GIH][hapmap]
rs2433132	1.00[ASN][1000 genomes]
rs34297214	1.00[ASN][1000 genomes]
rs4314865	1.00[ASN][1000 genomes]
rs55977919	1.00[ASN][1000 genomes]
rs56923458	1.00[ASN][1000 genomes]
rs57035146	1.00[ASN][1000 genomes]
rs57329980	1.00[ASN][1000 genomes]
rs58435034	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60806351	1.00[ASN][1000 genomes]
rs6426928	1.00[CHD][hapmap]
rs6668102	1.00[CHD][hapmap]
rs6681	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6690818	1.00[CHD][hapmap]
rs6700316	1.00[ASN][1000 genomes]
rs72698040	1.00[ASN][1000 genomes]
rs7355084	1.00[CHD][hapmap]
rs7551594	1.00[CHD][hapmap]
rs9333370	1.00[ASN][1000 genomes]
rs9333379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333470	1.00[ASN][1000 genomes]
rs9333475	1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9333372	RXRG	cis	parietal	SCAN
rs9333372	PEA15	cis	parietal	SCAN
rs9333372	PVRL4	cis	parietal	SCAN

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	chr1:165599400-165600800	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr1:165599400-165601400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:165599400-165601400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr1:165599400-165601400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:165599400-165601400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:165599400-165601400	Active TSS	Colon Smooth Muscle	Colon
32	chr1:165599400-165601400	Active TSS	Placenta	Placenta
33	chr1:165599400-165601400	Active TSS	Pancreas	Pancrea
34	chr1:165599400-165601400	Active TSS	HSMMtube	muscle
35	chr1:165599400-165601600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:165599400-165601600	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:165599400-165601600	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr1:165599400-165601600	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr1:165599400-165601600	Active TSS	Stomach Mucosa	stomach
40	chr1:165599400-165601800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:165599400-165601800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr1:165599400-165601800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:165599400-165601800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:165599400-165601800	Active TSS	Fetal Kidney	kidney
45	chr1:165599400-165602000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:165599400-165602000	Active TSS	Colonic Mucosa	Colon
47	chr1:165599400-165602200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:165599400-165602400	Active TSS	Ovary	ovary
49	chr1:165599400-165602400	Active TSS	Stomach Smooth Muscle	stomach
50	chr1:165599400-165602600	Active TSS	Right Ventricle	heart

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