Variant report

Variant	rs28452456
Chromosome Location	chr1:153520804-153520805
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr1:153520467-153520849	K562	blood:	n/a	n/a
2	RCOR1	chr1:153520533-153520812	Hela-S3	cervix:	n/a	n/a
3	BCL3	chr1:153520184-153521139	A549	lung:	n/a	n/a
4	MAZ	chr1:153520549-153520898	K562	blood:	n/a	chr1:153520680-153520690
5	CTCF	chr1:153520780-153521111	K562	blood:	n/a	n/a
6	POLR2A	chr1:153520367-153521451	K562	blood:	n/a	n/a
7	MAX	chr1:153520479-153521037	K562	blood:	n/a	chr1:153520680-153520690
8	MAX	chr1:153519483-153522520	A549	lung:	n/a	chr1:153520680-153520690
9	RCOR1	chr1:153520550-153520850	K562	blood:	n/a	n/a
10	POLR2A	chr1:153517452-153526571	MCF10A-Er-Src	breast:	n/a	n/a
11	RCOR1	chr1:153520454-153520848	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153520801-153520851	HCT-116	colon:	n/a
2	chr1:153520801-153520851	A549	lung:	n/a
3	chr1:153520801-153520851	SAEC	small airway:	n/a
4	chr1:153520801-153520851	GM12892	blood:	n/a
5	chr1:153520801-153520851	H1-hESC	embryonic stem cell:	embryo
6	chr1:153520801-153520851	GM06990	blood:	n/a
7	chr1:153520801-153520851	AoSMC	blood vessel:	n/a
8	chr1:153520801-153520851	SK-N-SH_RA	brain:	n/a
9	chr1:153520801-153520851	T-47D	breast:	n/a
10	chr1:153520801-153520851	HEEpiC	esophagus:	n/a
11	chr1:153520801-153520851	NB4	blood:	n/a
12	chr1:153520801-153520851	MCF-7	breast:	n/a
13	chr1:153520801-153520851	HEK293	kidney:	embryo
14	chr1:153520801-153520851	HIPEpiC	eye:	n/a
15	chr1:153520801-153520851	NHBE	bronchial:	n/a
16	chr1:153520801-153520851	PANC-1	pancreas:	n/a
17	chr1:153520801-153520851	GM12891	blood:	n/a
18	chr1:153520801-153520851	AG09309	skin:	n/a
19	chr1:153520801-153520851	CMK	blood:	n/a
20	chr1:153520801-153520851	Jurkat	blood:	n/a
21	chr1:153520801-153520851	GM19239	blood:	n/a
22	chr1:153520801-153520851	HRPEpiC	eye:	n/a
23	chr1:153520801-153520851	HepG2	liver:	n/a
24	chr1:153520801-153520851	HAEpiC	amniotic membrane:	n/a
25	chr1:153520801-153520851	HRE	kidney:	n/a
26	chr1:153520801-153520851	U87	brain:	n/a
27	chr1:153520801-153520851	SKMC	muscle:	n/a
28	chr1:153520801-153520851	HCM	heart:	n/a
29	chr1:153520801-153520851	K562	blood:	n/a
30	chr1:153520801-153520851	HCF	heart:	n/a
31	chr1:153520801-153520851	MCF10A-Er-Src	breast:	n/a
32	chr1:153520801-153520851	SK-N-MC	brain:	n/a
33	chr1:153520801-153520851	GM12878	blood:	n/a
34	chr1:153520801-153520851	RPTEC	kidney:	n/a
35	chr1:153520801-153520851	ovcar-3	ovarian:	n/a
36	chr1:153520801-153520851	Hepatocyte	liver:	n/a
37	chr1:153520801-153520851	HRCEpiC	kidney:	n/a
38	chr1:153520801-153520851	HL-60	blood:	n/a
39	chr1:153520801-153520851	HUVEC	blood vessel:	n/a
40	chr1:153520801-153520851	NH-A	brain:	n/a
41	chr1:153520801-153520851	LNCaP	prostate:	n/a
42	chr1:153520801-153520851	PrEC	prostate:	n/a
43	chr1:153520801-153520851	HMEC	breast:	n/a
44	chr1:153520801-153520851	SK-N-SH	brain:	n/a
45	chr1:153520801-153520851	AG04449	skin:	fetal
46	chr1:153520801-153520851	AG09319	gingival:	n/a
47	chr1:153520801-153520851	NT2-D1	testis:	n/a
48	chr1:153520801-153520851	ProgFib	skin:	n/a
49	chr1:153520801-153520851	NHDF-neo	bronchial:	n/a
50	chr1:153520801-153520851	HNPCEpiC	eye:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153518586..153521432-chr1:153521639..153523247,2	K562	blood:
2	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
3	chr1:153518882..153521795-chr1:153587475..153590405,3	MCF-7	breast:
4	chr1:153518586..153521432-chr1:153521623..153523247,3	K562	blood:
5	chr1:153514095..153517799-chr1:153518495..153521571,4	K562	blood:
6	chr1:153519212..153523090-chr1:153584863..153588698,4	MCF-7	breast:
7	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
8	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:

No data

Variant related genes	Relation type
S100A4	TF binding region
S100A4	CpG island
ENSG00000188015	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000189334	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1047325	0.91[EUR][1000 genomes]
rs1050923	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11488669	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16835437	0.91[EUR][1000 genomes]
rs16835455	0.91[EUR][1000 genomes]
rs1810765	0.82[EUR][1000 genomes]
rs28548347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594230	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28689606	0.97[EUR][1000 genomes]
rs28718953	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36022742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3762268	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41265160	0.80[AFR][1000 genomes]
rs41265162	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41265164	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4595398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55955983	0.94[EUR][1000 genomes]
rs56043239	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56057245	0.84[EUR][1000 genomes]
rs56089062	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56350425	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56838169	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57024596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58056804	0.97[EUR][1000 genomes]
rs58072118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59376279	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60218214	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60287468	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60969679	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61265945	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61558997	0.91[EUR][1000 genomes]
rs6427301	0.94[EUR][1000 genomes]
rs6671398	0.88[EUR][1000 genomes]
rs6700310	0.91[EUR][1000 genomes]
rs73026350	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74115473	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74115476	0.91[EUR][1000 genomes]
rs743687	0.82[EUR][1000 genomes]
rs7535476	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8401	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153509400-153527600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:153512400-153522400	Enhancers	Stomach Mucosa	stomach
3	chr1:153515400-153522800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:153515400-153523000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:153516800-153521800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:153516800-153522000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:153516800-153522400	Enhancers	Fetal Intestine Small	intestine
8	chr1:153517200-153522400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:153517400-153524000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:153517600-153522800	Enhancers	Spleen	Spleen
11	chr1:153518000-153522600	Enhancers	Fetal Stomach	stomach
12	chr1:153518200-153521000	Weak transcription	HUVEC	blood vessel
13	chr1:153518200-153521800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:153518200-153521800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:153518200-153523000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:153518200-153524000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:153518200-153524000	Enhancers	K562	blood
18	chr1:153518400-153521000	Weak transcription	NH-A	brain
19	chr1:153518400-153522200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:153518400-153522800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:153518400-153523800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:153518600-153521000	Weak transcription	Osteobl	bone
23	chr1:153518600-153521200	Enhancers	HSMM	muscle
24	chr1:153518600-153521400	Weak transcription	Psoas Muscle	Psoas
25	chr1:153518600-153521400	Weak transcription	Small Intestine	intestine
26	chr1:153518600-153521600	Weak transcription	GM12878-XiMat	blood
27	chr1:153518600-153521800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:153518600-153522000	Weak transcription	Gastric	stomach
29	chr1:153518600-153522400	Weak transcription	Fetal Lung	lung
30	chr1:153518600-153522400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:153518600-153522800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:153518600-153523600	Enhancers	Fetal Thymus	thymus
33	chr1:153518600-153524000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr1:153518600-153524000	Enhancers	Placenta	Placenta
35	chr1:153518600-153524200	Enhancers	Lung	lung
36	chr1:153518800-153521600	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr1:153518800-153523200	Enhancers	Right Atrium	heart
38	chr1:153518800-153524200	Enhancers	Esophagus	oesophagus
39	chr1:153519000-153521400	Weak transcription	Fetal Intestine Large	intestine
40	chr1:153519000-153522800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:153519000-153524400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:153519200-153521400	Weak transcription	Thymus	Thymus
43	chr1:153519200-153522000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr1:153519200-153522000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:153519200-153522400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:153519200-153523400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:153519200-153524000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:153519200-153524200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:153519200-153524400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr1:153519400-153522800	Enhancers	NHLF	lung

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