Variant report

Variant	rs4074436
Chromosome Location	chr1:154531910-154531911
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	RELA	chr1:154531167-154532436	GM18505	blood:	n/a	n/a
2	STAT1	chr1:154531165-154532414	GM12878	blood:	n/a	n/a
3	CHD2	chr1:154531152-154532272	K562	blood:	n/a	n/a
4	RAD21	chr1:154531873-154532427	H1-hESC	embryonic stem cell:	n/a	chr1:154532151-154532170 chr1:154532372-154532385
5	POLR2A	chr1:154531362-154532449	GM12891	blood:	n/a	n/a
6	MAX	chr1:154531136-154532333	Hela-S3	cervix:	n/a	chr1:154531276-154531285 chr1:154531356-154531366 chr1:154531184-154531194 chr1:154531279-154531287
7	RAD21	chr1:154531903-154532396	SK-N-SH_RA	brain:	n/a	chr1:154532151-154532170 chr1:154532372-154532385
8	BRCA1	chr1:154531310-154532172	HepG2	liver:	n/a	n/a
9	JUND	chr1:154531128-154532285	K562	blood:	n/a	chr1:154531326-154531335
10	MAFK	chr1:154531221-154532275	Hela-S3	cervix:	n/a	chr1:154532045-154532060 chr1:154531682-154531698
11	TCF12	chr1:154530961-154532280	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr1:154530846-154532332	H1-neurons	neurons:	n/a	n/a
13	TCF12	chr1:154530967-154531955	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:154531081-154532324	GM12878	blood:	n/a	n/a
15	MYC	chr1:154531055-154532385	K562	blood:	n/a	chr1:154531276-154531285 chr1:154531356-154531366 chr1:154531184-154531194 chr1:154531279-154531287
16	POLR2A	chr1:154530645-154532297	GM18951	blood:	n/a	n/a
17	MAX	chr1:154531107-154532274	GM12878	blood:	n/a	chr1:154531276-154531285 chr1:154531356-154531366 chr1:154531184-154531194 chr1:154531279-154531287
18	USF1	chr1:154530967-154532324	HCT-116	colon:	n/a	chr1:154531270-154531291 chr1:154531276-154531285 chr1:154531277-154531286 chr1:154531274-154531287 chr1:154531459-154531470 chr1:154531203-154531219 chr1:154531276-154531285
19	POLR2A	chr1:154531125-154532397	Hela-S3	cervix:	n/a	n/a
20	E2F4	chr1:154531134-154532292	K562	blood:	n/a	chr1:154531210-154531220 chr1:154531321-154531332 chr1:154531967-154531974 chr1:154531323-154531330 chr1:154531967-154531974 chr1:154531366-154531376 chr1:154531967-154531974 chr1:154531535-154531544 chr1:154531532-154531544 chr1:154531323-154531330 chr1:154531322-154531330 chr1:154531323-154531330 chr1:154531322-154531334 chr1:154531260-154531269
21	MAZ	chr1:154531028-154532314	Hela-S3	cervix:	n/a	chr1:154531276-154531285 chr1:154531184-154531194 chr1:154531279-154531287
22	GATA3	chr1:154530934-154531969	A549	lung:	n/a	n/a
23	MYC	chr1:154531017-154532512	A549	lung:	n/a	chr1:154531276-154531285 chr1:154531356-154531366 chr1:154531184-154531194 chr1:154531279-154531287
24	ZNF143	chr1:154531225-154532352	H1-hESC	embryonic stem cell:	n/a	chr1:154531521-154531531
25	MAFK	chr1:154531335-154532349	HepG2	liver:	n/a	chr1:154532045-154532060 chr1:154531682-154531698
26	MAZ	chr1:154530601-154532317	K562	blood:	n/a	chr1:154531276-154531285 chr1:154531184-154531194 chr1:154531279-154531287
27	POLR2A	chr1:154530952-154532339	HCT-116	colon:	n/a	n/a
28	BHLHE40	chr1:154531103-154532376	GM12878	blood:	n/a	chr1:154531270-154531291 chr1:154531276-154531285 chr1:154531277-154531286 chr1:154531274-154531287 chr1:154531203-154531219 chr1:154531276-154531285
29	YY1	chr1:154530958-154532344	ECC-1	luminal epithelium:	n/a	chr1:154531535-154531544 chr1:154531206-154531217 chr1:154531153-154531161 chr1:154531161-154531170 chr1:154531203-154531217 chr1:154531183-154531197 chr1:154531142-154531164 chr1:154531147-154531166 chr1:154531255-154531269 chr1:154531159-154531173
30	POLR2A	chr1:154531064-154531917	U87	brain:	n/a	n/a
31	GTF2F1	chr1:154531185-154532275	H1-hESC	embryonic stem cell:	n/a	n/a
32	USF1	chr1:154530933-154532435	HCT-116	colon:	n/a	chr1:154531270-154531291 chr1:154531276-154531285 chr1:154531277-154531286 chr1:154531274-154531287 chr1:154531459-154531470 chr1:154531203-154531219 chr1:154531276-154531285
33	REST	chr1:154531908-154532406	PFSK-1	brain:	n/a	chr1:154532005-154532018
34	SMARCB1	chr1:154531135-154532220	Hela-S3	cervix:	n/a	n/a
35	RCOR1	chr1:154531778-154532307	GM12878	blood:	n/a	n/a
36	USF1	chr1:154531049-154531930	K562	blood:	n/a	chr1:154531270-154531291 chr1:154531276-154531285 chr1:154531277-154531286 chr1:154531274-154531287 chr1:154531459-154531470 chr1:154531203-154531219 chr1:154531276-154531285
37	ZBTB7A	chr1:154530969-154532351	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr1:154531284-154532332	K562	blood:	n/a	n/a
39	ELK1	chr1:154531100-154532336	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:154530322-154532394	HepG2	liver:	n/a	n/a
41	NRF1	chr1:154530956-154532343	SK-N-SH	brain:	n/a	chr1:154531535-154531544 chr1:154531442-154531453 chr1:154531057-154531066
42	POLR2A	chr1:154531070-154531934	U87	brain:	n/a	n/a
43	CEBPB	chr1:154531629-154532287	H1-hESC	embryonic stem cell:	n/a	chr1:154532243-154532260
44	RCOR1	chr1:154531178-154532381	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:154530587-154532397	GM12892	blood:	n/a	n/a
46	ELF1	chr1:154531907-154532207	A549	lung:	n/a	n/a
47	SREBP1	chr1:154531065-154532672	GM12878	blood:	n/a	chr1:154531276-154531285 chr1:154531276-154531285
48	MXI1	chr1:154531139-154532427	Hela-S3	cervix:	n/a	chr1:154531305-154531314
49	POLR2A	chr1:154530994-154532256	MCF10A-Er-Src	breast:	n/a	n/a
50	E2F6	chr1:154531104-154532333	K562	blood:	n/a	chr1:154531210-154531220 chr1:154531967-154531974 chr1:154531323-154531330 chr1:154531967-154531974 chr1:154531366-154531376 chr1:154531967-154531974 chr1:154531535-154531544 chr1:154531532-154531544 chr1:154531323-154531330 chr1:154531322-154531330 chr1:154531323-154531330 chr1:154531322-154531334 chr1:154531260-154531269

No.	Distal block	Cell Line	Cell type
1	chr1:154473384..154476326-chr1:154529885..154532539,2	MCF-7	breast:
2	chr1:154531510..154533485-chr1:154539706..154542838,3	MCF-7	breast:
3	chr1:154163875..154165876-chr1:154529636..154532185,2	MCF-7	breast:
4	chr1:154505955..154508916-chr1:154529670..154532236,2	K562	blood:
5	chr1:154529667..154532782-chr1:154942768..154945185,3	MCF-7	breast:
6	chr1:154531125..154531942-chr10:35415007..35415704,2	Hela-S3	cervix:
7	chr1:154531579..154532180-chr1:154850720..154851668,3	K562	blood:
8	chr1:154191162..154194521-chr1:154529038..154532016,3	MCF-7	breast:
9	chr1:154531786..154532424-chr1:154721263..154721855,3	MCF-7	breast:
10	chr1:154531670..154532759-chr1:154732301..154733673,8	MCF-7	breast:
11	chr1:154531772..154532575-chr1:154989868..154990469,3	K562	blood:
12	chr1:154528898..154533098-chr1:154907799..154911445,7	MCF-7	breast:
13	chr1:154529703..154532693-chr1:155057067..155059987,2	K562	blood:
14	chr1:154530639..154532673-chr1:154599012..154601442,2	K562	blood:
15	chr1:154531587..154533271-chr1:154842628..154845356,2	K562	blood:
16	chr1:154530233..154532966-chr1:154538204..154541561,3	K562	blood:
17	chr1:154529028..154532359-chr1:155034427..155037689,4	MCF-7	breast:
18	chr1:154529257..154532572-chr1:154598516..154601356,4	MCF-7	breast:
19	chr1:154530233..154533708-chr1:154538204..154541561,4	K562	blood:
20	chr1:154531434..154533129-chr1:154974211..154976130,2	MCF-7	breast:
21	chr1:154529929..154534088-chr1:154598976..154602957,6	MCF-7	breast:
22	chr1:154528881..154534687-chr1:154578685..154583746,8	MCF-7	breast:
23	chr1:154450828..154453659-chr1:154529713..154531945,2	MCF-7	breast:

Variant related genes	Relation type
UBE2Q1	TF binding region
ENSG00000160710	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000163239	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000160716	Chromatin interaction
ENSG00000143603	Chromatin interaction
ENSG00000273110	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000230534	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000169291	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10752642	0.96[GIH][hapmap]
rs11265622	0.86[LWK][hapmap]
rs11265627	0.96[GIH][hapmap]
rs11265634	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12136771	0.86[LWK][hapmap]
rs12568083	0.86[LWK][hapmap]
rs14021	0.96[GIH][hapmap]
rs2280781	0.85[EUR][1000 genomes]
rs41302545	0.91[ASN][1000 genomes]
rs4474240	0.96[GIH][hapmap]
rs4478801	0.86[LWK][hapmap]
rs4845378	0.84[EUR][1000 genomes]
rs4845649	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4845652	0.91[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55908418	0.87[EUR][1000 genomes]
rs56047170	0.93[ASN][1000 genomes]
rs61811370	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61811371	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61811372	0.88[EUR][1000 genomes]
rs6427716	0.96[GIH][hapmap]
rs6660775	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6670375	0.96[GIH][hapmap]
rs6684921	0.86[LWK][hapmap]
rs6687112	0.96[GIH][hapmap]
rs6691727	0.96[GIH][hapmap]
rs6700296	0.86[LWK][hapmap]
rs72698182	0.87[EUR][1000 genomes]
rs7513603	0.96[GIH][hapmap]
rs7539745	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7543174	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs7550664	1.00[ASN][1000 genomes]
rs7553602	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9427082	0.90[ASN][1000 genomes]
rs9427415	0.96[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers 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 target site	65 gene(s)	inside rSNPs	diseases
3	esv3392983	chr1:154529853-154532901	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
4	esv3407675	chr1:154530078-154532176	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4074436	UBE2Q1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154528800-154532000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:154529000-154532200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:154529200-154532000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:154529200-154532200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:154529400-154532200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:154529600-154532000	Active TSS	Aorta	Aorta
7	chr1:154529600-154532200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:154529800-154532000	Active TSS	Lung	lung
9	chr1:154530200-154532000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:154530200-154532000	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr1:154530200-154532200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:154530200-154532200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:154530200-154532200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:154530200-154532200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:154530200-154532200	Active TSS	Fetal Kidney	kidney
16	chr1:154530400-154532000	Active TSS	Gastric	stomach
17	chr1:154530400-154532000	Active TSS	Ovary	ovary
18	chr1:154530400-154532000	Active TSS	Psoas Muscle	Psoas
19	chr1:154530400-154532000	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr1:154530400-154532000	Active TSS	Small Intestine	intestine
21	chr1:154530600-154532000	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr1:154530600-154532000	Active TSS	Brain Substantia Nigra	brain
23	chr1:154530600-154532000	Active TSS	Thymus	Thymus
24	chr1:154530600-154532200	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:154530600-154532200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:154531400-154532000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:154531400-154532200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr1:154531400-154532200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr1:154531400-154532200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:154531400-154532200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:154531400-154532200	Flanking Active TSS	Fetal Brain Male	brain
32	chr1:154531400-154532200	Flanking Active TSS	HUVEC	blood vessel
33	chr1:154531600-154532000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr1:154531600-154532000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:154531600-154532000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:154531600-154532000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:154531600-154532000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:154531600-154532000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:154531600-154532000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:154531600-154532000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr1:154531600-154532000	Flanking Active TSS	Fetal Brain Female	brain
42	chr1:154531600-154532000	Flanking Active TSS	Placenta	Placenta
43	chr1:154531600-154532000	Flanking Active TSS	Fetal Stomach	stomach
44	chr1:154531600-154532000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
45	chr1:154531600-154532000	Flanking Active TSS	HSMMtube	muscle
46	chr1:154531600-154532200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:154531600-154532200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:154531600-154532200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:154531600-154532200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:154531600-154532200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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