Variant report

Variant	rs540817051
Chromosome Location	chr1:45189762-45189763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:45188683-45189779	GM12878	blood:	n/a	chr1:45189379-45189392
2	MAX	chr1:45188846-45190776	NB4	blood:	n/a	n/a
3	POLR2A	chr1:45188746-45191415	HL-60	blood:	n/a	n/a
4	POLR2A	chr1:45188772-45191165	HL-60	blood:	n/a	n/a
5	MYC	chr1:45188879-45190790	NB4	blood:	n/a	n/a
6	POLR2A	chr1:45188941-45190728	NB4	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45189743-45189793	HRE	kidney:	n/a
2	chr1:45189743-45189793	HUVEC	blood vessel:	n/a
3	chr1:45189743-45189793	Jurkat	blood:	n/a
4	chr1:45189743-45189793	SKMC	muscle:	n/a
5	chr1:45189743-45189793	CMK	blood:	n/a
6	chr1:45189743-45189793	Caco-2	colon:	n/a
7	chr1:45189743-45189793	GM19239	blood:	n/a
8	chr1:45189743-45189793	ECC-1	luminal epithelium:	n/a
9	chr1:45189743-45189793	K562	blood:	n/a
10	chr1:45189743-45189793	ProgFib	skin:	n/a
11	chr1:45189743-45189793	HMEC	breast:	n/a
12	chr1:45189743-45189793	SK-N-SH	brain:	n/a
13	chr1:45189743-45189793	AoSMC	blood vessel:	n/a
14	chr1:45189743-45189793	AG10803	skin:	n/a
15	chr1:45189743-45189793	MCF10A-Er-Src	breast:	n/a
16	chr1:45189743-45189793	LNCaP	prostate:	n/a
17	chr1:45189743-45189793	PrEC	prostate:	n/a
18	chr1:45189743-45189793	NT2-D1	testis:	n/a
19	chr1:45189743-45189793	NB4	blood:	n/a
20	chr1:45189743-45189793	AG04449	skin:	fetal
21	chr1:45189743-45189793	HL-60	blood:	n/a
22	chr1:45189743-45189793	HCPEpiC	choroid plexus:	n/a
23	chr1:45189743-45189793	SK-N-MC	brain:	n/a
24	chr1:45189743-45189793	PFSK-1	brain:	n/a
25	chr1:45189743-45189793	IMR90	lung:	fetal
26	chr1:45189743-45189793	GM12892	blood:	n/a
27	chr1:45189743-45189793	SAEC	small airway:	n/a
28	chr1:45189743-45189793	HepG2	liver:	n/a
29	chr1:45189743-45189793	PANC-1	pancreas:	n/a
30	chr1:45189743-45189793	U87	brain:	n/a
31	chr1:45189743-45189793	Hepatocyte	liver:	n/a
32	chr1:45189743-45189793	NHBE	bronchial:	n/a
33	chr1:45189743-45189793	AG04450	lung:	fetal
34	chr1:45189743-45189793	HCF	heart:	n/a
35	chr1:45189743-45189793	GM06990	blood:	n/a
36	chr1:45189743-45189793	MCF-7	breast:	n/a
37	chr1:45189743-45189793	HPAEpiC	pulmonary alveolar:	n/a
38	chr1:45189743-45189793	AG09309	skin:	n/a
39	chr1:45189743-45189793	HAEpiC	amniotic membrane:	n/a
40	chr1:45189743-45189793	A549	lung:	n/a
41	chr1:45189743-45189793	NH-A	brain:	n/a
42	chr1:45189743-45189793	T-47D	breast:	n/a
43	chr1:45189743-45189793	HNPCEpiC	eye:	n/a
44	chr1:45189743-45189793	HRCEpiC	kidney:	n/a
45	chr1:45189743-45189793	HIPEpiC	eye:	n/a
46	chr1:45189743-45189793	GM12878	blood:	n/a
47	chr1:45189743-45189793	H1-hESC	embryonic stem cell:	embryo
48	chr1:45189743-45189793	NHDF-neo	bronchial:	n/a
49	chr1:45189743-45189793	HEK293	kidney:	embryo
50	chr1:45189743-45189793	ovcar-3	ovarian:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45184712..45189957-chr1:45986029..45989344,7	K562	blood:
2	chr1:45095364..45099259-chr1:45185766..45189852,13	K562	blood:
3	chr1:45179633..45191596-chr1:45283435..45288613,20	MCF-7	breast:
4	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:
5	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
6	chr1:45183794..45190315-chr1:45281186..45287888,32	MCF-7	breast:
7	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF2C-3	chr1:45189657-45190034	NONHSAT002889

No data

Variant related genes	Relation type
RNU5F-1	TF binding region
C1orf228	TF binding region
C1orf228	CpG island
RNU5F-1	CpG island
ENSG00000222009	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000117425	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
7	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
8	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
9	esv3375806	chr1:45189190-45191738	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45174400-45190400	Weak transcription	Lung	lung
2	chr1:45181200-45194800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:45184000-45191000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:45185200-45190600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:45185200-45192400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:45185600-45192200	Weak transcription	NHDF-Ad	bronchial
7	chr1:45185600-45194800	Weak transcription	Dnd41	blood
8	chr1:45186000-45190200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:45186200-45192400	Weak transcription	HSMM	muscle
10	chr1:45187800-45196200	Weak transcription	Right Atrium	heart
11	chr1:45188000-45190800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:45188000-45191000	Weak transcription	HepG2	liver
13	chr1:45188000-45192400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:45188000-45192400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:45188000-45192400	Weak transcription	A549	lung
16	chr1:45188000-45192400	Weak transcription	Osteobl	bone
17	chr1:45188000-45195800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:45188200-45190800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:45188600-45190800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:45188600-45190800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:45188800-45189800	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr1:45188800-45189800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr1:45188800-45189800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:45188800-45189800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:45188800-45189800	Enhancers	Liver	Liver
26	chr1:45188800-45189800	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:45188800-45190000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:45188800-45190000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr1:45188800-45190000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:45188800-45190000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:45188800-45190000	Flanking Active TSS	GM12878-XiMat	blood
32	chr1:45188800-45190200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr1:45188800-45190200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr1:45188800-45190200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr1:45188800-45190600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr1:45188800-45190800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr1:45188800-45190800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:45188800-45190800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:45189000-45189800	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr1:45189000-45189800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:45189000-45190000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr1:45189000-45190000	Flanking Active TSS	Fetal Thymus	thymus
43	chr1:45189000-45191200	Enhancers	Spleen	Spleen
44	chr1:45189200-45189800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:45189200-45189800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr1:45189400-45189800	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:45189400-45190000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:45189400-45190400	Active TSS	Thymus	Thymus
49	chr1:45189400-45190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:45189400-45192000	Weak transcription	K562	blood

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