Variant report

Variant	rs1509616
Chromosome Location	chr11:24518441-24518442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr11:24518245-24518979	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr11:24518372-24518886	H1-hESC	embryonic stem cell:	n/a	chr11:24518503-24518512 chr11:24518552-24518561
3	SIN3A	chr11:24517887-24519074	H1-hESC	embryonic stem cell:	n/a	chr11:24517970-24517979 chr11:24518886-24518899 chr11:24518623-24518632
4	POLR2A	chr11:24518223-24519132	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:24518345-24518785	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr11:24518221-24518926	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr11:24518440-24518590	HCM	heart:	n/a	n/a
8	POLR2A	chr11:24517880-24519103	H1-neurons	neurons:	n/a	n/a
9	RAD21	chr11:24518025-24518845	IMR90	lung:	n/a	n/a
10	RAD21	chr11:24518185-24519011	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr11:24518079-24518958	H1-hESC	embryonic stem cell:	n/a	chr11:24518489-24518499
12	REST	chr11:24517861-24519541	H1-neurons	neurons:	n/a	chr11:24518976-24518983 chr11:24518703-24518712
13	MAX	chr11:24518235-24518842	SK-N-SH	brain:	n/a	chr11:24518489-24518499
14	CTCF	chr11:24518380-24518530	HUVEC	blood vessel:	n/a	n/a
15	MAZ	chr11:24517782-24518819	IMR90	lung:	n/a	chr11:24518489-24518499
16	TAF1	chr11:24518249-24519003	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr11:24518425-24519050	H1-hESC	embryonic stem cell:	n/a	chr11:24519038-24519048 chr11:24519037-24519050
18	TAF1	chr11:24518284-24519076	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr11:24518247-24519049	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr11:24518250-24519001	H1-hESC	embryonic stem cell:	n/a	chr11:24518489-24518499
21	BACH1	chr11:24518280-24518908	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr11:24517881-24519463	SK-N-SH	brain:	n/a	chr11:24517948-24517957 chr11:24519038-24519048 chr11:24519037-24519050
23	POLR2A	chr11:24517952-24519162	H1-neurons	neurons:	n/a	n/a
24	ATF2	chr11:24518353-24518812	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr11:24518281-24518973	SK-N-SH_RA	brain:	n/a	n/a
26	ATF2	chr11:24518327-24518833	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOXP2	chr11:24518335-24518972	PFSK-1	brain:	n/a	n/a
28	CTCF	chr11:24518440-24518516	MCF-7	breast:	n/a	n/a
29	RAD21	chr11:24518225-24519135	H1-hESC	embryonic stem cell:	n/a	chr11:24519038-24519048 chr11:24519037-24519050
30	POLR2A	chr11:24518215-24518753	Gliobla	brain:	n/a	n/a
31	TBP	chr11:24518202-24518994	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr11:24518363-24518978	MCF-7	breast:	n/a	n/a
33	JUND	chr11:24518362-24518974	H1-hESC	embryonic stem cell:	n/a	chr11:24518591-24518600 chr11:24518372-24518381

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:24518414-24518464	HCT-116	colon:	n/a
2	chr11:24518414-24518464	BJ	skin:	n/a
3	chr11:24518414-24518464	H1-hESC	embryonic stem cell:	embryo
4	chr11:24518414-24518464	HMEC	breast:	n/a
5	chr11:24518414-24518464	SAEC	small airway:	n/a
6	chr11:24518414-24518464	MCF10A-Er-Src	breast:	n/a
7	chr11:24518414-24518464	HRE	kidney:	n/a
8	chr11:24518414-24518464	HL-60	blood:	n/a
9	chr11:24518414-24518464	MCF-7	breast:	n/a
10	chr11:24518414-24518464	GM06990	blood:	n/a
11	chr11:24518414-24518464	AG04449	skin:	fetal
12	chr11:24518414-24518464	T-47D	breast:	n/a
13	chr11:24518414-24518464	GM19239	blood:	n/a
14	chr11:24518414-24518464	Hepatocyte	liver:	n/a
15	chr11:24518414-24518464	HIPEpiC	eye:	n/a
16	chr11:24518414-24518464	HUVEC	blood vessel:	n/a
17	chr11:24518414-24518464	Jurkat	blood:	n/a
18	chr11:24518414-24518464	HCM	heart:	n/a
19	chr11:24518414-24518464	HRCEpiC	kidney:	n/a
20	chr11:24518414-24518464	SK-N-MC	brain:	n/a
21	chr11:24518414-24518464	NHDF-neo	bronchial:	n/a
22	chr11:24518414-24518464	AoSMC	blood vessel:	n/a
23	chr11:24518414-24518464	BE2_C	brain:	n/a
24	chr11:24518414-24518464	AG10803	skin:	n/a
25	chr11:24518414-24518464	HPAEpiC	pulmonary alveolar:	n/a
26	chr11:24518414-24518464	U87	brain:	n/a
27	chr11:24518414-24518464	ovcar-3	ovarian:	n/a
28	chr11:24518414-24518464	NB4	blood:	n/a
29	chr11:24518414-24518464	PFSK-1	brain:	n/a
30	chr11:24518414-24518464	HEEpiC	esophagus:	n/a
31	chr11:24518414-24518464	HepG2	liver:	n/a
32	chr11:24518414-24518464	IMR90	lung:	fetal
33	chr11:24518414-24518464	LNCaP	prostate:	n/a
34	chr11:24518414-24518464	NT2-D1	testis:	n/a
35	chr11:24518414-24518464	HCPEpiC	choroid plexus:	n/a
36	chr11:24518414-24518464	GM12891	blood:	n/a
37	chr11:24518414-24518464	HRPEpiC	eye:	n/a
38	chr11:24518414-24518464	NHBE	bronchial:	n/a
39	chr11:24518414-24518464	AG09319	gingival:	n/a
40	chr11:24518414-24518464	HAEpiC	amniotic membrane:	n/a
41	chr11:24518414-24518464	Hela-S3	cervix:	n/a
42	chr11:24518414-24518464	PANC-1	pancreas:	n/a
43	chr11:24518414-24518464	Caco-2	colon:	n/a
44	chr11:24518414-24518464	A549	lung:	n/a
45	chr11:24518414-24518464	HCF	heart:	n/a
46	chr11:24518414-24518464	RPTEC	kidney:	n/a
47	chr11:24518414-24518464	SK-N-SH_RA	brain:	n/a
48	chr11:24518414-24518464	HEK293	kidney:	embryo
49	chr11:24518414-24518464	SKMC	muscle:	n/a
50	chr11:24518414-24518464	CMK	blood:	n/a

No data

Variant related genes	Relation type
LUZP2	TF binding region
LUZP2	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11027951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11027956	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1509586	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2403956	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35175729	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7109828	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7111245	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7927293	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7928417	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055026	chr11:24151133-24737122	Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1037744	chr11:24174588-24737122	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv467755	chr11:24407381-24527958	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv553791	chr11:24407381-24527958	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv897088	chr11:24419481-24543475	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv553794	chr11:24435202-24537624	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1837793	chr11:24443570-24527958	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv897089	chr11:24477706-24545353	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv553819	chr11:24499370-24545353	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv469945	chr11:24515523-24545353	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:24517200-24518800	Active TSS	Brain Angular Gyrus	brain
2	chr11:24517200-24519200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr11:24517200-24519600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
4	chr11:24517400-24518600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:24517400-24520000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr11:24517600-24519400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr11:24517800-24518800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:24517800-24518800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
9	chr11:24517800-24519000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:24517800-24519000	Bivalent/Poised TSS	NHLF	lung
11	chr11:24517800-24519200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
12	chr11:24517800-24519200	Active TSS	Right Ventricle	heart
13	chr11:24517800-24519400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:24517800-24519400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:24517800-24519400	Active TSS	Brain Cingulate Gyrus	brain
16	chr11:24517800-24519400	Bivalent/Poised TSS	NH-A	brain
17	chr11:24517800-24519600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr11:24517800-24519600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr11:24517800-24519600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr11:24517800-24519800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr11:24517800-24519800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr11:24517800-24520200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr11:24518000-24518600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:24518000-24518600	Active TSS	Colonic Mucosa	Colon
25	chr11:24518000-24518600	Bivalent Enhancer	Placenta	Placenta
26	chr11:24518000-24518600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
27	chr11:24518000-24518600	Bivalent/Poised TSS	HMEC	breast
28	chr11:24518000-24518800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:24518000-24518800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
30	chr11:24518000-24518800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
31	chr11:24518000-24518800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
32	chr11:24518000-24519000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:24518000-24519000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:24518000-24519000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:24518000-24519000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:24518000-24519000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr11:24518000-24519000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:24518000-24519000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:24518000-24519000	Active TSS	Rectal Smooth Muscle	rectum
40	chr11:24518000-24519000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
41	chr11:24518000-24519200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:24518000-24519200	Active TSS	Fetal Brain Male	brain
43	chr11:24518000-24519200	Active TSS	Fetal Heart	heart
44	chr11:24518000-24519200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
45	chr11:24518000-24519400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr11:24518000-24519400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr11:24518000-24519400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:24518000-24519400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:24518000-24519400	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr11:24518000-24519400	Bivalent/Poised TSS	Fetal Kidney	kidney

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