Variant report

Variant	rs1038745
Chromosome Location	chr1:151966745-151966746
allele	A/C
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	JUND	chr1:151964679-151967014	A549	lung:	n/a	chr1:151965116-151965124 chr1:151964989-151964998 chr1:151965114-151965126
2	SP1	chr1:151964375-151967094	HCT-116	colon:	n/a	chr1:151966108-151966117 chr1:151965093-151965103 chr1:151965093-151965103 chr1:151964597-151964611 chr1:151966145-151966158
3	ZBTB7A	chr1:151966683-151966885	K562	blood:	n/a	n/a
4	POLR2A	chr1:151964626-151967011	A549	lung:	n/a	n/a
5	YY1	chr1:151966153-151966842	ECC-1	luminal epithelium:	n/a	chr1:151966492-151966503 chr1:151966343-151966352
6	ESR1	chr1:151966306-151966959	ECC-1	luminal epithelium:	n/a	n/a
7	ZBTB7A	chr1:151965503-151967022	ECC-1	luminal epithelium:	n/a	chr1:151965986-151965995
8	POLR2A	chr1:151964557-151966771	PFSK-1	brain:	n/a	n/a
9	TEAD4	chr1:151966125-151966989	ECC-1	luminal epithelium:	n/a	n/a
10	STAT3	chr1:151966523-151966768	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr1:151963929-151968128	A549	lung:	n/a	chr1:151964984-151964991
12	JUND	chr1:151964469-151967138	MCF-7	breast:	n/a	chr1:151965116-151965124 chr1:151964989-151964998 chr1:151965114-151965126
13	FOXM1	chr1:151966199-151967090	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr1:151964643-151966990	A549	lung:	n/a	n/a
15	TAF1	chr1:151964138-151966844	A549	lung:	n/a	n/a
16	ZKSCAN1	chr1:151964686-151966857	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr1:151966620-151966770	MCF-7	breast:	n/a	n/a
18	BRCA1	chr1:151966498-151966910	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:151966415-151966898	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:151964030-151967233	Hela-S3	cervix:	n/a	n/a
21	GATA3	chr1:151964354-151967404	MCF-7	breast:	n/a	chr1:151964995-151965005 chr1:151966769-151966776 chr1:151966893-151966901 chr1:151964477-151964493 chr1:151964482-151964489 chr1:151964988-151964997 chr1:151964482-151964489 chr1:151964482-151964489
22	POLR2A	chr1:151964053-151966959	ECC-1	luminal epithelium:	n/a	n/a
23	ELF1	chr1:151964192-151967139	MCF-7	breast:	n/a	n/a
24	FOXA1	chr1:151966176-151966958	T-47D	breast:	n/a	n/a
25	GATA3	chr1:151966033-151966923	T-47D	breast:	n/a	chr1:151966769-151966776 chr1:151966893-151966901
26	USF1	chr1:151966016-151966943	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr1:151964752-151966939	A549	lung:	n/a	n/a
28	EP300	chr1:151966028-151966816	T-47D	breast:	n/a	chr1:151966728-151966741
29	TAF1	chr1:151964723-151966899	ECC-1	luminal epithelium:	n/a	n/a
30	TEAD4	chr1:151963975-151967080	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr1:151966620-151966770	HBMEC	blood vessel:	n/a	n/a
32	CHD1	chr1:151963720-151967191	IMR90	lung:	n/a	n/a
33	GATA3	chr1:151964047-151967118	A549	lung:	n/a	chr1:151964995-151965005 chr1:151966769-151966776 chr1:151966893-151966901 chr1:151964286-151964297 chr1:151964477-151964493 chr1:151964482-151964489 chr1:151964988-151964997 chr1:151964482-151964489 chr1:151964482-151964489
34	MAX	chr1:151966046-151966900	SK-N-SH	brain:	n/a	chr1:151966738-151966745 chr1:151966205-151966214
35	FOS	chr1:151966608-151966808	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr1:151960197-151968028	U87	brain:	n/a	n/a
37	POLR2A	chr1:151966419-151966824	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr1:151966110-151967019	ECC-1	luminal epithelium:	n/a	chr1:151966738-151966745 chr1:151966205-151966214
39	POLR2A	chr1:151963122-151967069	PANC-1	pancreas:	n/a	n/a
40	USF2	chr1:151966637-151966837	H1-hESC	embryonic stem cell:	n/a	n/a
41	USF1	chr1:151966595-151966849	H1-hESC	embryonic stem cell:	n/a	n/a
42	TCF12	chr1:151964665-151967078	ECC-1	luminal epithelium:	n/a	chr1:151964984-151964991
43	GABPA	chr1:151964182-151967200	MCF-7	breast:	n/a	chr1:151966653-151966667
44	MAX	chr1:151966407-151966925	H1-hESC	embryonic stem cell:	n/a	chr1:151966738-151966745
45	MYC	chr1:151966662-151966798	MCF-7	breast:	n/a	chr1:151966738-151966745
46	MYC	chr1:151966565-151966888	MCF-7	breast:	n/a	chr1:151966738-151966745
47	GATA3	chr1:151964212-151967251	MCF-7	breast:	n/a	chr1:151964995-151965005 chr1:151966769-151966776 chr1:151966893-151966901 chr1:151964286-151964297 chr1:151964477-151964493 chr1:151964482-151964489 chr1:151964988-151964997 chr1:151964482-151964489 chr1:151964482-151964489
48	POLR2A	chr1:151964734-151966786	MCF-7	breast:	n/a	n/a
49	ESR1	chr1:151966237-151966991	ECC-1	luminal epithelium:	n/a	n/a
50	CTCF	chr1:151966620-151966770	SAEC	small airway:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151961745..151973594-chr1:152015769..152025096,31	MCF-7	breast:
2	chr1:151879131..151885542-chr1:151961269..151968730,13	MCF-7	breast:
3	chr1:151966480..151967337-chr5:138629507..138630472,2	Hela-S3	cervix:
4	chr1:149856742..149859715-chr1:151963697..151967031,3	MCF-7	breast:
5	chr1:151966036..151966766-chr19:571248..572063,2	Hela-S3	cervix:
6	chr1:151966344..151967208-chr17:48784695..48785497,2	Hela-S3	cervix:
7	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
8	chr1:151880209..151887387-chr1:151961986..151968084,15	MCF-7	breast:
9	chr1:151965119..151967469-chr3:64007952..64010141,2	MCF-7	breast:
10	chr1:151966177..151966960-chr3:49203200..49203840,2	Hela-S3	cervix:

Variant related genes	Relation type
NBPF18P	TF binding region
S100A10	TF binding region
ENSG00000178096	Chromatin interaction
ENSG00000172270	Chromatin interaction
ENSG00000267751	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000154945	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000015479	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs41264560	1.00[AMR][1000 genomes]
rs41265240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845417	1.00[AMR][1000 genomes]
rs4845720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845722	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845724	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
5	esv3377930	chr1:151965153-151967701	Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151963200-151967000	Active TSS	Right Atrium	heart
2	chr1:151963400-151966800	Active TSS	Esophagus	oesophagus
3	chr1:151963600-151966800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:151963600-151967000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:151963600-151967000	Active TSS	Placenta Amnion	Placenta Amnion
6	chr1:151964000-151966800	Active TSS	Fetal Intestine Large	intestine
7	chr1:151964000-151967400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:151964200-151966800	Active TSS	Sigmoid Colon	Sigmoid Colon
9	chr1:151964400-151966800	Active TSS	Lung	lung
10	chr1:151964400-151966800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:151964400-151967000	Active TSS	Gastric	stomach
12	chr1:151964400-151967200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:151964400-151967200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:151964600-151966800	Active TSS	Fetal Intestine Small	intestine
15	chr1:151964600-151966800	Active TSS	Ovary	ovary
16	chr1:151964600-151967000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:151964600-151967000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:151964600-151967000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:151964600-151967000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:151964600-151967200	Active TSS	Brain Anterior Caudate	brain
21	chr1:151964600-151967600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:151964800-151966800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:151964800-151966800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:151964800-151966800	Active TSS	NHDF-Ad	bronchial
25	chr1:151964800-151967000	Active TSS	Aorta	Aorta
26	chr1:151965000-151966800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:151965000-151966800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:151965000-151966800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:151965000-151967000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr1:151965000-151967200	Active TSS	Colon Smooth Muscle	Colon
31	chr1:151965200-151966800	Active TSS	Left Ventricle	heart
32	chr1:151965200-151967000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr1:151965200-151967400	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:151965400-151966800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:151965400-151966800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:151965400-151967000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:151965400-151967200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr1:151965400-151967200	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:151965400-151967200	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:151965600-151966800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:151965600-151966800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
42	chr1:151965600-151966800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr1:151965600-151966800	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr1:151965600-151967000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr1:151965600-151967200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr1:151965600-151967200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:151965800-151967000	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr1:151965800-151967200	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:151965800-151967600	Active TSS	A549	lung
50	chr1:151966000-151966800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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