Variant report

Variant	rs25687
Chromosome Location	chr1:45243311-45243312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:45243018-45243342	HL-60	blood:	n/a	n/a
2	TEAD4	chr1:45242942-45243549	K562	blood:	n/a	n/a
3	POLR2A	chr1:45240631-45247540	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45240526-45248028	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:45242869-45243669	K562	blood:	n/a	n/a
6	CTCF	chr1:45243139-45243487	T-47D	breast:	n/a	n/a
7	POLR2A	chr1:45242280-45243426	HUVEC	blood vessel:	n/a	n/a
8	ZKSCAN1	chr1:45243258-45243561	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:45242853-45243434	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:45243230-45243643	GM12878	blood:	n/a	n/a
11	SIX5	chr1:45243216-45243571	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:45243263-45243550	A549	lung:	n/a	n/a
13	POLR2A	chr1:45242949-45243653	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:45240483-45248016	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:45240295-45248263	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:45242580-45247462	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:45240547-45249219	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
19	ZBTB33	chr1:45243174-45243901	K562	blood:	n/a	n/a
20	HEY1	chr1:45240514-45243580	K562	blood:	n/a	n/a
21	POLR2A	chr1:45242522-45244255	SK-N-SH	brain:	n/a	n/a
22	EP300	chr1:45243203-45243561	T-47D	breast:	n/a	n/a
23	POLR2A	chr1:45242766-45248217	GM12891	blood:	n/a	n/a
24	REST	chr1:45243281-45243484	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr1:45242928-45247383	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:45242972-45243686	HCT-116	colon:	n/a	n/a
27	MTA3	chr1:45242861-45243362	GM12878	blood:	n/a	n/a
28	GATA3	chr1:45243227-45243553	T-47D	breast:	n/a	n/a
29	POLR2A	chr1:45240546-45248272	GM12892	blood:	n/a	n/a
30	REST	chr1:45243233-45243471	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:45242888-45243670	HCT-116	colon:	n/a	n/a
32	NFATC1	chr1:45242885-45243544	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:45242629-45247224	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:45242989-45243639	U87	brain:	n/a	n/a
35	POLR2A	chr1:45240631-45243638	GM12878	blood:	n/a	n/a
36	SP1	chr1:45243136-45243844	H1-hESC	embryonic stem cell:	n/a	n/a
37	NR2F2	chr1:45242741-45243327	MCF-7	breast:	n/a	n/a
38	POLR2A	chr1:45242979-45245039	K562	blood:	n/a	n/a
39	POLR2A	chr1:45242691-45243650	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:45242745-45243389	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr1:45243078-45243541	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:45242783-45244071	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr1:45240508-45247317	GM12878	blood:	n/a	n/a
44	NR2F2	chr1:45241656-45243726	K562	blood:	n/a	n/a
45	POLR2A	chr1:45240713-45247745	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr1:45243002-45243575	GM12891	blood:	n/a	n/a
47	POLR2A	chr1:45243001-45245051	HepG2	liver:	n/a	n/a
48	POLR2A	chr1:45240271-45247480	K562	blood:	n/a	n/a
49	ZNF263	chr1:45243071-45243573	HEK293-T-REx	kidney:	n/a	n/a
50	POLR2A	chr1:45243082-45243569	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45243311-45243361	AG09309	skin:	n/a
2	chr1:45243311-45243361	U87	brain:	n/a
3	chr1:45243311-45243361	GM12892	blood:	n/a
4	chr1:45243311-45243361	PrEC	prostate:	n/a
5	chr1:45243311-45243361	NB4	blood:	n/a
6	chr1:45243311-45243361	SK-N-SH	brain:	n/a
7	chr1:45243311-45243361	BJ	skin:	n/a
8	chr1:45243311-45243361	HCPEpiC	choroid plexus:	n/a
9	chr1:45243311-45243361	HCF	heart:	n/a
10	chr1:45243311-45243361	HEEpiC	esophagus:	n/a
11	chr1:45243311-45243361	HL-60	blood:	n/a
12	chr1:45243311-45243361	GM19239	blood:	n/a
13	chr1:45243311-45243361	ProgFib	skin:	n/a
14	chr1:45243311-45243361	NH-A	brain:	n/a
15	chr1:45243311-45243361	HepG2	liver:	n/a
16	chr1:45243311-45243361	NHDF-neo	bronchial:	n/a
17	chr1:45243311-45243361	PFSK-1	brain:	n/a
18	chr1:45243311-45243361	HAEpiC	amniotic membrane:	n/a
19	chr1:45243311-45243361	HRE	kidney:	n/a
20	chr1:45243311-45243361	CMK	blood:	n/a
21	chr1:45243311-45243361	BE2_C	brain:	n/a
22	chr1:45243311-45243361	HPAEpiC	pulmonary alveolar:	n/a
23	chr1:45243311-45243361	HEK293	kidney:	embryo
24	chr1:45243311-45243361	H1-hESC	embryonic stem cell:	embryo
25	chr1:45243311-45243361	HNPCEpiC	eye:	n/a
26	chr1:45243311-45243361	PANC-1	pancreas:	n/a
27	chr1:45243311-45243361	SKMC	muscle:	n/a
28	chr1:45243311-45243361	RPTEC	kidney:	n/a
29	chr1:45243311-45243361	GM12891	blood:	n/a
30	chr1:45243311-45243361	SAEC	small airway:	n/a
31	chr1:45243311-45243361	NHBE	bronchial:	n/a
32	chr1:45243311-45243361	HRPEpiC	eye:	n/a
33	chr1:45243311-45243361	AG10803	skin:	n/a
34	chr1:45243311-45243361	T-47D	breast:	n/a
35	chr1:45243311-45243361	HCM	heart:	n/a
36	chr1:45243311-45243361	ECC-1	luminal epithelium:	n/a
37	chr1:45243311-45243361	MCF10A-Er-Src	breast:	n/a
38	chr1:45243311-45243361	IMR90	lung:	fetal
39	chr1:45243311-45243361	AG09319	gingival:	n/a
40	chr1:45243311-45243361	Caco-2	colon:	n/a
41	chr1:45243311-45243361	NT2-D1	testis:	n/a
42	chr1:45243311-45243361	MCF-7	breast:	n/a
43	chr1:45243311-45243361	Hela-S3	cervix:	n/a
44	chr1:45243311-45243361	Jurkat	blood:	n/a
45	chr1:45243311-45243361	GM06990	blood:	n/a
46	chr1:45243311-45243361	ovcar-3	ovarian:	n/a
47	chr1:45243311-45243361	GM12878	blood:	n/a
48	chr1:45243311-45243361	SK-N-MC	brain:	n/a
49	chr1:45243311-45243361	HCT-116	colon:	n/a
50	chr1:45243311-45243361	HUVEC	blood vessel:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45239429..45243402-chr1:45282541..45287001,15	MCF-7	breast:
2	chr1:45194515..45198714-chr1:45239955..45244261,13	MCF-7	breast:
3	chr1:45204011..45207083-chr1:45240823..45243671,4	MCF-7	breast:
4	chr1:45241279..45243837-chr1:45275916..45278923,3	MCF-7	breast:
5	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
6	chr1:45239592..45244618-chr1:45476667..45480609,10	K562	blood:
7	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
8	chr1:45239101..45240995-chr1:45242933..45244701,2	MCF-7	breast:
9	chr1:45239959..45246724-chr1:45282430..45287057,13	MCF-7	breast:
10	chr1:45239942..45244585-chr1:45273690..45277023,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225721	TF binding region
SNORD38B	TF binding region
SNORD38A	TF binding region
RPS8	TF binding region
SNORD38B	CpG island
ENSG00000225721	CpG island
SNORD38A	CpG island
RPS8	CpG island
ENSG00000117425	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000200169	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17883044	1.00[AMR][1000 genomes]
rs57175012	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60411293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6656623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7515879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
11	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 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	chr1:45240600-45244000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:45240800-45243600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:45241600-45243600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
4	chr1:45241600-45243800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
5	chr1:45241600-45244200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
6	chr1:45241600-45244200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:45241600-45244200	Transcr. at gene 5' and 3'	NHEK	skin
8	chr1:45241600-45244600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr1:45241600-45244600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
10	chr1:45241600-45244600	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr1:45241600-45244800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:45241800-45243400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:45241800-45243600	Transcr. at gene 5' and 3'	Right Ventricle	heart
14	chr1:45241800-45243600	Transcr. at gene 5' and 3'	Osteobl	bone
15	chr1:45241800-45244000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
16	chr1:45241800-45244200	Transcr. at gene 5' and 3'	NHLF	lung
17	chr1:45241800-45244800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:45241800-45244800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:45241800-45244800	Transcr. at gene 5' and 3'	A549	lung
20	chr1:45241800-45244800	Transcr. at gene 5' and 3'	K562	blood
21	chr1:45241800-45245000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
22	chr1:45242000-45243600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:45242000-45243600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
24	chr1:45242000-45243600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:45242000-45244000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
26	chr1:45242000-45244000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:45242000-45244200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:45242000-45244400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
29	chr1:45242000-45244600	Transcr. at gene 5' and 3'	HepG2	liver
30	chr1:45242000-45245000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:45242000-45245000	Transcr. at gene 5' and 3'	Hela-S3	cervix
32	chr1:45242200-45243400	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
33	chr1:45242200-45243400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
34	chr1:45242200-45243400	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
35	chr1:45242200-45243600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:45242200-45244000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:45242200-45244000	Transcr. at gene 5' and 3'	HMEC	breast
38	chr1:45242200-45244400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
39	chr1:45242200-45244600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:45242200-45244600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:45242200-45244800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
42	chr1:45242400-45243400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:45242400-45243400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr1:45242400-45243600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:45242400-45243600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:45242400-45243600	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
47	chr1:45242400-45243600	Genic enhancers	Spleen	Spleen
48	chr1:45242400-45244000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
49	chr1:45242400-45244600	Transcr. at gene 5' and 3'	NH-A	brain
50	chr1:45242400-45244800	Genic enhancers	Stomach Mucosa	stomach

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