Variant report

Variant	rs559163495
Chromosome Location	chr1:190447427-190447428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr1:190447257-190447673	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr1:190447354-190447781	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr1:190447319-190447458	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr1:190447380-190447530	HPF	lung:	n/a	n/a
5	CTBP2	chr1:190447174-190448394	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:190447360-190447510	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr1:190447349-190447460	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:190447234-190447510	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:190447340-190447490	HPAF	blood vessel:	n/a	n/a
10	FOXA1	chr1:190447415-190447980	T-47D	breast:	n/a	n/a
11	CTCF	chr1:190447300-190447450	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr1:190447280-190447430	HBMEC	blood vessel:	n/a	n/a
13	CTCF	chr1:190447340-190447490	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr1:190447313-190447519	MCF-7	breast:	n/a	n/a
15	EBF1	chr1:190447422-190448028	GM12878	blood:	n/a	chr1:190447604-190447617 chr1:190447912-190447925 chr1:190447606-190447616 chr1:190447605-190447616 chr1:190447606-190447615 chr1:190447914-190447923 chr1:190447914-190447924 chr1:190447606-190447615 chr1:190447914-190447923
16	CTCF	chr1:190447280-190447430	HAc	cerebellar:	n/a	n/a
17	NRF1	chr1:190447353-190447456	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr1:190447092-190447680	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr1:190447364-190447505	MCF-7	breast:	n/a	n/a
20	SIN3A	chr1:190447141-190448398	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr1:190447425-190447949	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr1:190447278-190447521	Gliobla	brain:	n/a	n/a
23	POLR2A	chr1:190447267-190448073	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr1:190447320-190447470	HCPEpiC	choroid plexus:	n/a	n/a
25	CTCF	chr1:190447320-190447470	Caco-2	colon:	n/a	n/a
26	MYC	chr1:190447387-190447515	MCF-7	breast:	n/a	n/a
27	CTCF	chr1:190447380-190447530	HRPEpiC	eye:	n/a	n/a
28	CTCF	chr1:190447393-190447440	GM12891	blood:	n/a	n/a
29	CTCF	chr1:190447340-190447490	NHDF-neo	bronchial:	n/a	n/a
30	CTCF	chr1:190447360-190447510	AoAF	blood vessel:	n/a	n/a
31	POLR2A	chr1:190446856-190447801	H1-neurons	neurons:	n/a	n/a
32	CTCF	chr1:190447360-190447510	AG04450	lung:	n/a	n/a
33	CTCF	chr1:190447360-190447510	HA-sp	spinal cord:	n/a	n/a
34	CTCF	chr1:190447312-190447506	MCF-7	breast:	n/a	n/a
35	REST	chr1:190446596-190448409	H1-neurons	neurons:	n/a	chr1:190447480-190447493 chr1:190448080-190448087 chr1:190447477-190447490 chr1:190447462-190447480 chr1:190447339-190447352 chr1:190447792-190447805 chr1:190447332-190447345
36	POLR2A	chr1:190447323-190447571	MCF-7	breast:	n/a	n/a
37	CTCF	chr1:190447377-190447504	MCF-7	breast:	n/a	n/a
38	CTCF	chr1:190447332-190447535	A549	lung:	n/a	n/a
39	CTCF	chr1:190447320-190447470	HBMEC	blood vessel:	n/a	n/a
40	GATA2	chr1:190446768-190448262	SH-SY5Y	brain:	n/a	n/a
41	POLR2A	chr1:190447352-190447448	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr1:190447320-190447470	HRE	kidney:	n/a	n/a
43	MYC	chr1:190447341-190447525	MCF-7	breast:	n/a	n/a
44	POLR2A	chr1:190447237-190448114	H1-neurons	neurons:	n/a	n/a
45	CTCF	chr1:190447380-190447530	HRE	kidney:	n/a	n/a
46	CTCF	chr1:190447321-190447536	MCF-7	breast:	n/a	n/a
47	JUND	chr1:190447168-190448270	H1-hESC	embryonic stem cell:	n/a	chr1:190447519-190447527
48	TCF7L2	chr1:190446979-190448068	HCT-116	colon:	n/a	n/a
49	CTCF	chr1:190447360-190447510	HRPEpiC	eye:	n/a	n/a
50	ZNF143	chr1:190447295-190448099	H1-hESC	embryonic stem cell:	n/a	chr1:190447438-190447456 chr1:190447337-190447355

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:190447421-190447471	HNPCEpiC	eye:	n/a
2	chr1:190447421-190447471	T-47D	breast:	n/a
3	chr1:190447421-190447471	AG04450	lung:	fetal
4	chr1:190447421-190447471	PrEC	prostate:	n/a
5	chr1:190447421-190447471	HIPEpiC	eye:	n/a
6	chr1:190447421-190447471	AG09309	skin:	n/a
7	chr1:190447421-190447471	ovcar-3	ovarian:	n/a
8	chr1:190447421-190447471	Caco-2	colon:	n/a
9	chr1:190447421-190447471	H1-hESC	embryonic stem cell:	embryo
10	chr1:190447421-190447471	HUVEC	blood vessel:	n/a
11	chr1:190447421-190447471	HCPEpiC	choroid plexus:	n/a
12	chr1:190447421-190447471	SKMC	muscle:	n/a
13	chr1:190447421-190447471	CMK	blood:	n/a
14	chr1:190447421-190447471	HMEC	breast:	n/a
15	chr1:190447421-190447471	GM12878	blood:	n/a
16	chr1:190447421-190447471	NHBE	bronchial:	n/a
17	chr1:190447421-190447471	HEEpiC	esophagus:	n/a
18	chr1:190447421-190447471	ECC-1	luminal epithelium:	n/a
19	chr1:190447421-190447471	NT2-D1	testis:	n/a
20	chr1:190447421-190447471	U87	brain:	n/a
21	chr1:190447421-190447471	ProgFib	skin:	n/a
22	chr1:190447421-190447471	AG09319	gingival:	n/a
23	chr1:190447421-190447471	RPTEC	kidney:	n/a
24	chr1:190447421-190447471	A549	lung:	n/a
25	chr1:190447421-190447471	AG10803	skin:	n/a
26	chr1:190447421-190447471	HCF	heart:	n/a
27	chr1:190447421-190447471	NH-A	brain:	n/a
28	chr1:190447421-190447471	PFSK-1	brain:	n/a
29	chr1:190447421-190447471	K562	blood:	n/a
30	chr1:190447421-190447471	GM12891	blood:	n/a
31	chr1:190447421-190447471	HRCEpiC	kidney:	n/a
32	chr1:190447421-190447471	HepG2	liver:	n/a
33	chr1:190447421-190447471	HAEpiC	amniotic membrane:	n/a
34	chr1:190447421-190447471	Jurkat	blood:	n/a
35	chr1:190447421-190447471	MCF10A-Er-Src	breast:	n/a
36	chr1:190447421-190447471	SK-N-SH	brain:	n/a
37	chr1:190447421-190447471	GM12892	blood:	n/a
38	chr1:190447421-190447471	IMR90	lung:	fetal
39	chr1:190447421-190447471	PANC-1	pancreas:	n/a
40	chr1:190447421-190447471	AoSMC	blood vessel:	n/a
41	chr1:190447421-190447471	LNCaP	prostate:	n/a
42	chr1:190447421-190447471	Hepatocyte	liver:	n/a
43	chr1:190447421-190447471	GM06990	blood:	n/a
44	chr1:190447421-190447471	SK-N-MC	brain:	n/a
45	chr1:190447421-190447471	HL-60	blood:	n/a
46	chr1:190447421-190447471	BE2_C	brain:	n/a
47	chr1:190447421-190447471	MCF-7	breast:	n/a
48	chr1:190447421-190447471	HCM	heart:	n/a
49	chr1:190447421-190447471	HCT-116	colon:	n/a
50	chr1:190447421-190447471	HPAEpiC	pulmonary alveolar:	n/a

No data

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGS18-5	chr1:190447356-190447622	XLOC_000505
2	lnc-RGS18-5	chr1:190446965-190447761	NONHSAT008497
3	lnc-RGS18-5	chr1:190447329-190447761	NONHSAT008498
4	lnc-RGS18-5	chr1:190447390-190447622	XLOC_000505

No data

Variant related genes	Relation type
BRINP3	TF binding region
ENSG00000241505	TF binding region
ENSG00000237457	TF binding region
ENSG00000237457	CpG island
ENSG00000241505	CpG island
BRINP3	CpG island

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv872758	chr1:190351677-190510003	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872760	chr1:190377988-190577336	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872761	chr1:190389741-190485034	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv872762	chr1:190389741-190510003	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv872763	chr1:190389741-190531642	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv872764	chr1:190399946-190531642	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv872765	chr1:190418653-190464647	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv466750	chr1:190433413-190496007	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv548551	chr1:190433413-190496007	Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv466761	chr1:190433413-190545283	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv548552	chr1:190433413-190545283	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv466772	chr1:190446253-190492280	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv548553	chr1:190446253-190492280	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190440000-190448800	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:190440200-190448800	Active TSS	Fetal Intestine Large	intestine
3	chr1:190440800-190448600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:190440800-190448800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:190441200-190448600	Active TSS	Fetal Intestine Small	intestine
6	chr1:190441200-190448600	Active TSS	Right Atrium	heart
7	chr1:190443000-190449600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:190445000-190447600	Active TSS	Brain Angular Gyrus	brain
9	chr1:190445200-190449000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:190446200-190448800	Active TSS	Brain Germinal Matrix	brain
11	chr1:190446200-190449600	Active TSS	Brain Anterior Caudate	brain
12	chr1:190446200-190450000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:190446600-190447600	Active TSS	Colonic Mucosa	Colon
14	chr1:190446600-190447800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:190446600-190447800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:190446600-190448000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
17	chr1:190446600-190448400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:190446800-190447600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr1:190446800-190447800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:190446800-190448400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:190446800-190448400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:190446800-190448400	Active TSS	Rectal Smooth Muscle	rectum
23	chr1:190447000-190447600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:190447000-190447800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
25	chr1:190447000-190448200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
26	chr1:190447000-190448200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
27	chr1:190447000-190448400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:190447000-190448400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:190447000-190448400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:190447000-190448400	Bivalent/Poised TSS	Fetal Kidney	kidney
31	chr1:190447000-190448400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
32	chr1:190447000-190448400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
33	chr1:190447000-190448400	Bivalent/Poised TSS	A549	lung
34	chr1:190447000-190448600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:190447000-190448600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:190447000-190449400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:190447200-190447600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr1:190447200-190447600	Bivalent Enhancer	Aorta	Aorta
39	chr1:190447200-190447600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr1:190447200-190447600	Bivalent Enhancer	Placenta	Placenta
41	chr1:190447200-190447600	Flanking Active TSS	Psoas Muscle	Psoas
42	chr1:190447200-190447800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr1:190447200-190447800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr1:190447200-190447800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr1:190447200-190447800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:190447200-190447800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr1:190447200-190447800	Flanking Active TSS	Pancreas	Pancrea
48	chr1:190447200-190448000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:190447200-190448000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:190447200-190448000	Bivalent/Poised TSS	Fetal Lung	lung

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