Variant report

Variant	rs7539939
Chromosome Location	chr1:224803875-224803876
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:107)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:107 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr1:224803487-224804096	H1-hESC	embryonic stem cell:	n/a	chr1:224803931-224803947
2	KAP1	chr1:224803073-224803934	U2OS	brain:	n/a	n/a
3	CTCF	chr1:224803760-224803910	SK-N-SH_RA	brain:	n/a	n/a
4	SP1	chr1:224803466-224803875	H1-hESC	embryonic stem cell:	n/a	chr1:224803764-224803776 chr1:224803715-224803726 chr1:224803765-224803774
5	POLR2A	chr1:224803368-224805065	H1-neurons	neurons:	n/a	n/a
6	TBP	chr1:224803557-224804604	H1-hESC	embryonic stem cell:	n/a	n/a
7	GABPA	chr1:224803548-224803931	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr1:224803522-224803903	K562	blood:	n/a	chr1:224803735-224803742
9	POLR2A	chr1:224803509-224804303	HL-60	blood:	n/a	n/a
10	MYC	chr1:224803572-224803893	MCF10A-Er-Src	breast:	n/a	chr1:224803735-224803742
11	JUND	chr1:224803665-224803932	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr1:224803308-224804307	ECC-1	luminal epithelium:	n/a	chr1:224803735-224803742
13	USF1	chr1:224803488-224804179	SK-N-SH	brain:	n/a	chr1:224803661-224803677
14	CTCF	chr1:224803874-224803877	MCF-7	breast:	n/a	n/a
15	EP300	chr1:224803348-224804253	ECC-1	luminal epithelium:	n/a	chr1:224803931-224803947 chr1:224803486-224803502
16	POLR2A	chr1:224803604-224804225	ECC-1	luminal epithelium:	n/a	n/a
17	YY1	chr1:224803533-224804138	ECC-1	luminal epithelium:	n/a	chr1:224803668-224803679
18	E2F6	chr1:224803437-224804199	A549	lung:	n/a	chr1:224803938-224803952 chr1:224803665-224803675
19	POLR2A	chr1:224803654-224804254	U87	brain:	n/a	n/a
20	RAD21	chr1:224803373-224804078	SK-N-SH_RA	brain:	n/a	n/a
21	POLR2A	chr1:224803273-224805067	U87	brain:	n/a	n/a
22	CTCF	chr1:224803860-224804010	SK-N-SH_RA	brain:	n/a	n/a
23	MYC	chr1:224803545-224803997	MCF-7	breast:	n/a	chr1:224803735-224803742
24	SIN3AK20	chr1:224803751-224804107	PANC-1	pancreas:	n/a	n/a
25	KAP1	chr1:224803450-224804215	HEK293	kidney:	n/a	n/a
26	TAF1	chr1:224803402-224804006	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF12	chr1:224803526-224803876	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr1:224803306-224804426	ECC-1	luminal epithelium:	n/a	chr1:224803735-224803742
29	PBX3	chr1:224803412-224804306	SK-N-SH	brain:	n/a	n/a
30	SETDB1	chr1:224803496-224803886	U2OS	brain:	n/a	n/a
31	MYC	chr1:224803486-224803942	MCF-7	breast:	n/a	chr1:224803735-224803742
32	CTCF	chr1:224803860-224804010	HMF	breast:	n/a	n/a
33	MAX	chr1:224803432-224804291	NB4	blood:	n/a	chr1:224803735-224803742
34	CTCF	chr1:224803803-224803941	MCF-7	breast:	n/a	n/a
35	USF1	chr1:224803466-224804062	ECC-1	luminal epithelium:	n/a	chr1:224803661-224803677
36	POLR2A	chr1:224803273-224804619	U87	brain:	n/a	n/a
37	POLR2A	chr1:224803517-224804182	SK-N-SH	brain:	n/a	n/a
38	MAX	chr1:224803354-224804199	A549	lung:	n/a	chr1:224803735-224803742
39	SP4	chr1:224803485-224804019	H1-hESC	embryonic stem cell:	n/a	chr1:224803715-224803726
40	MAX	chr1:224803388-224804205	SK-N-SH	brain:	n/a	chr1:224803735-224803742
41	CTCF	chr1:224803800-224803950	Caco-2	colon:	n/a	n/a
42	CTCF	chr1:224803840-224803990	HBMEC	blood vessel:	n/a	n/a
43	MXI1	chr1:224803420-224804133	IMR90	lung:	n/a	n/a
44	POLR2A	chr1:224803677-224804161	MCF-7	breast:	n/a	n/a
45	CHD1	chr1:224803791-224803902	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD2	chr1:224803482-224804134	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr1:224803541-224803909	H1-hESC	embryonic stem cell:	n/a	chr1:224803735-224803742
48	POLR2A	chr1:224803530-224804255	U87	brain:	n/a	n/a
49	CTCF	chr1:224803760-224803910	Caco-2	colon:	n/a	n/a
50	YY1	chr1:224803485-224803900	H1-hESC	embryonic stem cell:	n/a	chr1:224803668-224803679

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:224803837-224803887	Hela-S3	cervix:	n/a
2	chr1:224803837-224803887	K562	blood:	n/a
3	chr1:224803837-224803887	NH-A	brain:	n/a
4	chr1:224803837-224803887	HRPEpiC	eye:	n/a
5	chr1:224803837-224803887	BE2_C	brain:	n/a
6	chr1:224803837-224803887	HEK293	kidney:	embryo
7	chr1:224803837-224803887	HPAEpiC	pulmonary alveolar:	n/a
8	chr1:224803837-224803887	AG10803	skin:	n/a
9	chr1:224803837-224803887	AG09319	gingival:	n/a
10	chr1:224803837-224803887	PrEC	prostate:	n/a
11	chr1:224803837-224803887	GM12878	blood:	n/a
12	chr1:224803837-224803887	LNCaP	prostate:	n/a
13	chr1:224803837-224803887	T-47D	breast:	n/a
14	chr1:224803837-224803887	HL-60	blood:	n/a
15	chr1:224803837-224803887	AG04450	lung:	fetal
16	chr1:224803837-224803887	IMR90	lung:	fetal
17	chr1:224803837-224803887	HNPCEpiC	eye:	n/a
18	chr1:224803837-224803887	NB4	blood:	n/a
19	chr1:224803837-224803887	AG04449	skin:	fetal
20	chr1:224803837-224803887	HMEC	breast:	n/a
21	chr1:224803837-224803887	Hepatocyte	liver:	n/a
22	chr1:224803837-224803887	HepG2	liver:	n/a
23	chr1:224803837-224803887	NHBE	bronchial:	n/a
24	chr1:224803837-224803887	HCM	heart:	n/a
25	chr1:224803837-224803887	PFSK-1	brain:	n/a
26	chr1:224803837-224803887	A549	lung:	n/a
27	chr1:224803837-224803887	MCF-7	breast:	n/a
28	chr1:224803837-224803887	HEEpiC	esophagus:	n/a
29	chr1:224803837-224803887	NT2-D1	testis:	n/a
30	chr1:224803837-224803887	U87	brain:	n/a
31	chr1:224803837-224803887	HCPEpiC	choroid plexus:	n/a
32	chr1:224803837-224803887	Caco-2	colon:	n/a
33	chr1:224803837-224803887	SKMC	muscle:	n/a
34	chr1:224803837-224803887	AoSMC	blood vessel:	n/a
35	chr1:224803837-224803887	ECC-1	luminal epithelium:	n/a
36	chr1:224803837-224803887	NHDF-neo	bronchial:	n/a
37	chr1:224803837-224803887	SK-N-SH	brain:	n/a
38	chr1:224803837-224803887	GM06990	blood:	n/a
39	chr1:224803837-224803887	GM19239	blood:	n/a
40	chr1:224803837-224803887	HIPEpiC	eye:	n/a
41	chr1:224803837-224803887	ovcar-3	ovarian:	n/a
42	chr1:224803837-224803887	HCT-116	colon:	n/a
43	chr1:224803837-224803887	HAEpiC	amniotic membrane:	n/a
44	chr1:224803837-224803887	SK-N-MC	brain:	n/a
45	chr1:224803837-224803887	BJ	skin:	n/a
46	chr1:224803837-224803887	MCF10A-Er-Src	breast:	n/a
47	chr1:224803837-224803887	SK-N-SH_RA	brain:	n/a
48	chr1:224803837-224803887	HCF	heart:	n/a
49	chr1:224803837-224803887	PANC-1	pancreas:	n/a
50	chr1:224803837-224803887	AG09309	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224760255..224762194-chr1:224803067..224805853,2	MCF-7	breast:
2	chr1:224803776..224804276-chr9:115875131..115875670,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR26-1	chr1:224803777-224803922	XLOC_001228

No data

Variant related genes	Relation type
CNIH3	TF binding region
CNIH3	CpG island
ENSG00000231528	Chromatin interaction
ENSG00000229991	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10799588	0.88[ASN][1000 genomes]
rs11802812	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11803050	1.00[AMR][1000 genomes]
rs11804994	1.00[AMR][1000 genomes]
rs16849654	1.00[JPT][hapmap]
rs57209437	0.93[ASN][1000 genomes]
rs58565730	0.93[ASN][1000 genomes]
rs59018094	0.80[ASN][1000 genomes]
rs59610983	0.93[ASN][1000 genomes]
rs59643307	0.93[ASN][1000 genomes]
rs61247305	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6657458	0.93[ASN][1000 genomes]
rs6693360	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7534595	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7550112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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 miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224803000-224804000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
2	chr1:224803000-224804000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:224803200-224804200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
4	chr1:224803200-224804400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
5	chr1:224803200-224804400	Active TSS	NHLF	lung
6	chr1:224803200-224804600	Bivalent Enhancer	Fetal Lung	lung
7	chr1:224803200-224805800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:224803200-224805800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:224803200-224806400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:224803200-224806400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
11	chr1:224803200-224807000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:224803200-224807000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:224803200-224807200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:224803200-224807400	Active TSS	NHDF-Ad	bronchial
15	chr1:224803400-224804000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
16	chr1:224803400-224804000	Bivalent Enhancer	Placenta	Placenta
17	chr1:224803400-224804000	Bivalent Enhancer	Left Ventricle	heart
18	chr1:224803400-224804000	Bivalent Enhancer	Lung	lung
19	chr1:224803400-224804000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
20	chr1:224803400-224804000	Bivalent/Poised TSS	Small Intestine	intestine
21	chr1:224803400-224804000	Bivalent Enhancer	Spleen	Spleen
22	chr1:224803400-224804200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr1:224803400-224804200	Flanking Bivalent TSS/Enh	Thymus	Thymus
24	chr1:224803400-224804400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
25	chr1:224803400-224804600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
26	chr1:224803400-224804600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
27	chr1:224803400-224804800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr1:224803400-224804800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:224803400-224805000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
30	chr1:224803400-224805000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:224803400-224805200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr1:224803400-224805200	Flanking Active TSS	Gastric	stomach
33	chr1:224803400-224805400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:224803400-224805800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:224803400-224805800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:224803400-224806800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr1:224803600-224804000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:224803600-224804000	Bivalent/Poised TSS	HepG2	liver
39	chr1:224803600-224804000	Bivalent/Poised TSS	HUVEC	blood vessel
40	chr1:224803600-224804200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:224803600-224804200	Enhancers	Liver	Liver
42	chr1:224803600-224804200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
43	chr1:224803600-224804200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
44	chr1:224803600-224804200	Bivalent/Poised TSS	NHEK	skin
45	chr1:224803600-224804200	Bivalent/Poised TSS	Osteobl	bone
46	chr1:224803600-224804400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr1:224803600-224804400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:224803600-224804400	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:224803600-224804400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:224803600-224804400	Bivalent/Poised TSS	Fetal Intestine Large	intestine

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