Variant report

Variant	rs541100959
Chromosome Location	chr18:29264532-29264533
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	POLR2A	chr18:29264463-29265680	HUVEC	blood vessel:	n/a	n/a
2	YY1	chr18:29264252-29264611	GM12892	blood:	n/a	chr18:29264415-29264429
3	CHD2	chr18:29264220-29264858	GM12878	blood:	n/a	chr18:29264724-29264734
4	POLR2A	chr18:29263962-29266139	GM18951	blood:	n/a	n/a
5	MAX	chr18:29264066-29266173	GM12878	blood:	n/a	n/a
6	PML	chr18:29263917-29266204	GM12878	blood:	n/a	n/a
7	YY1	chr18:29264311-29264567	K562	blood:	n/a	chr18:29264415-29264429
8	POLR2A	chr18:29264354-29266101	GM10847	blood:	n/a	n/a
9	SPI1	chr18:29264296-29264615	GM12878	blood:	n/a	chr18:29264390-29264397
10	POLR2A	chr18:29264493-29266183	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr18:29263952-29264846	H1-neurons	neurons:	n/a	chr18:29264801-29264814 chr18:29264809-29264822
12	MXI1	chr18:29264065-29265493	GM12878	blood:	n/a	n/a
13	POLR2A	chr18:29264160-29266130	GM12878	blood:	n/a	n/a
14	RCOR1	chr18:29264172-29264852	GM12878	blood:	n/a	n/a
15	TAF1	chr18:29264234-29264616	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3A	chr18:29263824-29266100	H1-hESC	embryonic stem cell:	n/a	chr18:29265439-29265452 chr18:29265145-29265158
17	POLR2A	chr18:29264143-29266339	GM18505	blood:	n/a	n/a
18	STAT5A	chr18:29264152-29264631	GM12878	blood:	n/a	n/a
19	MAX	chr18:29264051-29266252	A549	lung:	n/a	n/a
20	POLR2A	chr18:29264087-29265019	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr18:29264382-29265653	MCF-7	breast:	n/a	n/a
22	POLR2A	chr18:29264009-29266286	GM12892	blood:	n/a	n/a
23	POLR2A	chr18:29264318-29265533	Gliobla	brain:	n/a	n/a
24	POLR2A	chr18:29264346-29265559	A549	lung:	n/a	n/a
25	ZBTB7A	chr18:29264244-29265041	ECC-1	luminal epithelium:	n/a	n/a
26	SPI1	chr18:29264346-29264689	HL-60	blood:	n/a	chr18:29264390-29264397
27	TBP	chr18:29264361-29264896	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr18:29263761-29266391	GM19099	blood:	n/a	n/a
29	POLR2A	chr18:29263999-29266298	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr18:29264508-29266381	SK-N-SH	brain:	n/a	chr18:29265145-29265158
31	POLR2A	chr18:29264055-29264987	H1-neurons	neurons:	n/a	n/a
32	MAZ	chr18:29264223-29266189	GM12878	blood:	n/a	n/a
33	TAF7	chr18:29264356-29264940	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr18:29264033-29266166	GM18526	blood:	n/a	n/a
35	POLR2A	chr18:29264301-29264564	GM12878	blood:	n/a	n/a
36	EBF1	chr18:29264497-29264671	GM12878	blood:	n/a	chr18:29264513-29264524
37	POLR2A	chr18:29264128-29266113	GM12892	blood:	n/a	n/a
38	POLR2A	chr18:29264132-29266174	H1-hESC	embryonic stem cell:	n/a	n/a
39	SPI1	chr18:29264422-29264577	K562	blood:	n/a	n/a
40	ZNF263	chr18:29263898-29265483	HEK293-T-REx	kidney:	n/a	chr18:29264726-29264735 chr18:29264745-29264754
41	POLR2A	chr18:29263986-29264539	GM12878	blood:	n/a	n/a
42	SPI1	chr18:29264090-29264824	GM12878	blood:	n/a	chr18:29264390-29264397
43	WRNIP1	chr18:29263720-29264733	GM12878	blood:	n/a	n/a
44	POLR2A	chr18:29264251-29265812	HEK293	kidney:	n/a	n/a
45	MTA3	chr18:29263836-29264658	GM12878	blood:	n/a	n/a
46	POLR2A	chr18:29264212-29265535	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr18:29264111-29266224	GM19193	blood:	n/a	n/a
48	CHD2	chr18:29264393-29264845	Hela-S3	cervix:	n/a	chr18:29264724-29264734
49	ZBTB7A	chr18:29264334-29265041	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr18:29263608-29266533	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29235239..29238459-chr18:29263541..29266170,4	MCF-7	breast:

Variant related genes	Relation type
B4GALT6	TF binding region
ENSG00000259985	TF binding region
ENSG00000118276	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3344706	chr18:29263704-29266352	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr18:29261600-29265600	Active TSS	GM12878-XiMat	blood
2	chr18:29262000-29266200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr18:29262400-29265800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr18:29262600-29266400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr18:29262800-29265800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr18:29262800-29265800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr18:29262800-29265800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr18:29263000-29264600	Flanking Active TSS	Dnd41	blood
9	chr18:29263000-29265600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr18:29263000-29265800	Active TSS	Psoas Muscle	Psoas
11	chr18:29263000-29266000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:29263000-29266400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr18:29263200-29265600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr18:29263200-29265600	Active TSS	Primary T cells from cord blood	blood
15	chr18:29263200-29265600	Active TSS	Duodenum Mucosa	Duodenum
16	chr18:29263200-29265800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:29263200-29265800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:29263200-29266200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr18:29263200-29266200	Active TSS	Brain Angular Gyrus	brain
20	chr18:29263200-29266200	Active TSS	Brain Cingulate Gyrus	brain
21	chr18:29263200-29266400	Active TSS	Brain Anterior Caudate	brain
22	chr18:29263200-29266400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr18:29263400-29266200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:29263400-29266200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr18:29263600-29265600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr18:29263600-29265600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr18:29263600-29265800	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr18:29263600-29265800	Active TSS	Right Atrium	heart
29	chr18:29263600-29266000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr18:29263600-29266200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr18:29263600-29266200	Active TSS	Colon Smooth Muscle	Colon
32	chr18:29263600-29266600	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr18:29263800-29264600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr18:29263800-29265600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:29263800-29265600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:29263800-29265800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr18:29263800-29265800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr18:29263800-29265800	Active TSS	HMEC	breast
39	chr18:29263800-29265800	Active TSS	NHLF	lung
40	chr18:29263800-29266000	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr18:29263800-29266000	Active TSS	A549	lung
42	chr18:29263800-29266000	Active TSS	NHDF-Ad	bronchial
43	chr18:29264000-29264600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
44	chr18:29264000-29264600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
45	chr18:29264000-29264600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr18:29264000-29264600	Flanking Active TSS	Liver	Liver
47	chr18:29264000-29264600	Flanking Active TSS	Colonic Mucosa	Colon
48	chr18:29264000-29264600	Active TSS	Fetal Heart	heart
49	chr18:29264000-29264600	Flanking Active TSS	Fetal Thymus	thymus
50	chr18:29264000-29264600	Active TSS	Stomach Mucosa	stomach

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