Variant report

Variant	rs11542015
Chromosome Location	chr1:151966348-151966349
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	JUND	chr1:151964679-151967014	A549	lung:	n/a	chr1:151965116-151965124 chr1:151964989-151964998 chr1:151965114-151965126
2	TAF1	chr1:151966221-151966519	PFSK-1	brain:	n/a	n/a
3	SP1	chr1:151964375-151967094	HCT-116	colon:	n/a	chr1:151966108-151966117 chr1:151965093-151965103 chr1:151965093-151965103 chr1:151964597-151964611 chr1:151966145-151966158
4	EGR1	chr1:151966086-151966652	ECC-1	luminal epithelium:	n/a	chr1:151966340-151966350 chr1:151966108-151966118
5	TCF12	chr1:151966124-151966388	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:151964626-151967011	A549	lung:	n/a	n/a
7	YY1	chr1:151966153-151966842	ECC-1	luminal epithelium:	n/a	chr1:151966492-151966503 chr1:151966343-151966352
8	ESR1	chr1:151966306-151966959	ECC-1	luminal epithelium:	n/a	n/a
9	ZBTB7A	chr1:151965503-151967022	ECC-1	luminal epithelium:	n/a	chr1:151965986-151965995
10	POLR2A	chr1:151964557-151966771	PFSK-1	brain:	n/a	n/a
11	TEAD4	chr1:151966125-151966989	ECC-1	luminal epithelium:	n/a	n/a
12	TCF12	chr1:151963929-151968128	A549	lung:	n/a	chr1:151964984-151964991
13	JUND	chr1:151964469-151967138	MCF-7	breast:	n/a	chr1:151965116-151965124 chr1:151964989-151964998 chr1:151965114-151965126
14	POLR2A	chr1:151960317-151966352	A549	lung:	n/a	n/a
15	HMGN3	chr1:151966149-151966357	K562	blood:	n/a	n/a
16	FOXM1	chr1:151966199-151967090	ECC-1	luminal epithelium:	n/a	n/a
17	REST	chr1:151966085-151966457	PANC-1	pancreas:	n/a	chr1:151966105-151966118 chr1:151966108-151966121 chr1:151966103-151966113
18	POLR2A	chr1:151964643-151966990	A549	lung:	n/a	n/a
19	POLR2A	chr1:151964654-151966522	HUVEC	blood vessel:	n/a	n/a
20	TAF1	chr1:151964138-151966844	A549	lung:	n/a	n/a
21	ZKSCAN1	chr1:151964686-151966857	Hela-S3	cervix:	n/a	n/a
22	E2F4	chr1:151965794-151966640	MCF10A-Er-Src	breast:	n/a	chr1:151966343-151966352
23	TAF1	chr1:151966118-151966405	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr1:151966195-151966414	HepG2	liver:	n/a	chr1:151966205-151966214
25	POLR2A	chr1:151964030-151967233	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:151964780-151966620	ProgFib	skin:	n/a	n/a
27	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
28	POLR2A	chr1:151964053-151966959	ECC-1	luminal epithelium:	n/a	n/a
29	ELF1	chr1:151964192-151967139	MCF-7	breast:	n/a	n/a
30	TAF1	chr1:151966100-151966614	SK-N-SH	brain:	n/a	n/a
31	FOXA1	chr1:151966176-151966958	T-47D	breast:	n/a	n/a
32	GATA3	chr1:151966033-151966923	T-47D	breast:	n/a	chr1:151966769-151966776 chr1:151966893-151966901
33	USF1	chr1:151966016-151966943	ECC-1	luminal epithelium:	n/a	n/a
34	MYC	chr1:151966215-151966418	MCF-7	breast:	n/a	n/a
35	POLR2A	chr1:151964752-151966939	A549	lung:	n/a	n/a
36	POLR2A	chr1:151965488-151966409	H1-hESC	embryonic stem cell:	n/a	n/a
37	EP300	chr1:151966028-151966816	T-47D	breast:	n/a	chr1:151966728-151966741
38	TAF1	chr1:151964723-151966899	ECC-1	luminal epithelium:	n/a	n/a
39	TEAD4	chr1:151963975-151967080	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:151966104-151966415	SK-N-MC	brain:	n/a	n/a
41	CHD1	chr1:151963720-151967191	IMR90	lung:	n/a	n/a
42	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
43	MAX	chr1:151966046-151966900	SK-N-SH	brain:	n/a	chr1:151966738-151966745 chr1:151966205-151966214
44	POLR2A	chr1:151960197-151968028	U87	brain:	n/a	n/a
45	E2F6	chr1:151966182-151966396	K562	blood:	n/a	chr1:151966343-151966352
46	MAX	chr1:151966110-151967019	ECC-1	luminal epithelium:	n/a	chr1:151966738-151966745 chr1:151966205-151966214
47	POLR2A	chr1:151963122-151967069	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr1:151966108-151966398	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:151966124-151966398	HepG2	liver:	n/a	n/a
50	TCF12	chr1:151964665-151967078	ECC-1	luminal epithelium:	n/a	chr1:151964984-151964991

No.	Distal block	Cell Line	Cell type
1	chr1:151803084..151806304-chr1:151962981..151966430,4	MCF-7	breast:
2	chr1:151961745..151973594-chr1:152015769..152025096,31	MCF-7	breast:
3	chr1:151879131..151885542-chr1:151961269..151968730,13	MCF-7	breast:
4	chr1:151518156..151521130-chr1:151964781..151966696,2	MCF-7	breast:
5	chr1:149856742..149859715-chr1:151963697..151967031,3	MCF-7	breast:
6	chr1:151966103..151966694-chr20:30194806..30195732,2	Hela-S3	cervix:
7	chr1:151811113..151814780-chr1:151962857..151966577,5	MCF-7	breast:
8	chr1:151966036..151966766-chr19:571248..572063,2	Hela-S3	cervix:
9	chr1:151966344..151967208-chr17:48784695..48785497,2	Hela-S3	cervix:
10	chr1:151965797..151966383-chr9:34048318..34048939,2	NB4	blood:
11	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
12	chr1:151880209..151887387-chr1:151961986..151968084,15	MCF-7	breast:
13	chr1:151965119..151967469-chr3:64007952..64010141,2	MCF-7	breast:
14	chr1:151965647..151966378-chr11:17229031..17229603,2	Hela-S3	cervix:
15	chr1:151966177..151966960-chr3:49203200..49203840,2	Hela-S3	cervix:
16	chr1:151965905..151966596-chr6:43596733..43597724,2	Hela-S3	cervix:

Variant related genes	Relation type
NBPF18P	TF binding region
S100A10	TF binding region
ENSG00000154945	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000172270	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000011405	Chromatin interaction
ENSG00000137073	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000234614	Chromatin interaction
ENSG00000267751	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000201134	Chromatin interaction
ENSG00000264395	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1038747	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11204922	0.86[ASN][1000 genomes]
rs2338019	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932581	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2932586	0.88[AMR][1000 genomes]
rs2932590	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999508	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2999512	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2999526	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999528	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999531	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999534	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2999539	0.80[AMR][1000 genomes]
rs2999560	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3007708	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11542015	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs11542015	THEM4	cis	Esophagus Muscularis	GTEx
rs11542015	THEM4	cis	multi-tissue	Pritchard
rs11542015	S100A10	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:151964000-151966600	Active TSS	NHLF	lung
7	chr1:151964000-151966800	Active TSS	Fetal Intestine Large	intestine
8	chr1:151964000-151967400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:151964200-151966800	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr1:151964400-151966600	Active TSS	Colonic Mucosa	Colon
11	chr1:151964400-151966600	Active TSS	HSMM	muscle
12	chr1:151964400-151966800	Active TSS	Lung	lung
13	chr1:151964400-151966800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:151964400-151967000	Active TSS	Gastric	stomach
15	chr1:151964400-151967200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:151964400-151967200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:151964600-151966800	Active TSS	Fetal Intestine Small	intestine
18	chr1:151964600-151966800	Active TSS	Ovary	ovary
19	chr1:151964600-151967000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:151964600-151967000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:151964600-151967000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:151964600-151967000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:151964600-151967200	Active TSS	Brain Anterior Caudate	brain
24	chr1:151964600-151967600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr1:151964800-151966600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:151964800-151966600	Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:151964800-151966600	Active TSS	Hela-S3	cervix
28	chr1:151964800-151966600	Active TSS	HMEC	breast
29	chr1:151964800-151966800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:151964800-151966800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:151964800-151966800	Active TSS	NHDF-Ad	bronchial
32	chr1:151964800-151967000	Active TSS	Aorta	Aorta
33	chr1:151965000-151966400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:151965000-151966600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:151965000-151966600	Active TSS	Right Ventricle	heart
36	chr1:151965000-151966600	Active TSS	Small Intestine	intestine
37	chr1:151965000-151966600	Active TSS	HUVEC	blood vessel
38	chr1:151965000-151966600	Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:151965000-151966800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:151965000-151966800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:151965000-151966800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:151965000-151967000	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr1:151965000-151967200	Active TSS	Colon Smooth Muscle	Colon
44	chr1:151965200-151966400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr1:151965200-151966800	Active TSS	Left Ventricle	heart
46	chr1:151965200-151967000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr1:151965200-151967400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:151965400-151966400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:151965400-151966400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:151965400-151966400	Active TSS	HSMMtube	muscle

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