Variant report

Variant	rs56043239
Chromosome Location	chr1:153518483-153518484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:75)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:75 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153514448-153518753	Hela-S3	cervix:	n/a	n/a
2	RFX5	chr1:153517420-153518905	Hela-S3	cervix:	n/a	n/a
3	TAF1	chr1:153517349-153518609	A549	lung:	n/a	n/a
4	POLR2A	chr1:153517338-153518575	A549	lung:	n/a	n/a
5	POLR2A	chr1:153516727-153518754	SK-N-MC	brain:	n/a	n/a
6	REST	chr1:153517093-153518753	A549	lung:	n/a	chr1:153518621-153518634 chr1:153518563-153518576
7	MYC	chr1:153517401-153518597	Hela-S3	cervix:	n/a	n/a
8	BCL3	chr1:153517280-153518595	A549	lung:	n/a	n/a
9	YY1	chr1:153517104-153518644	A549	lung:	n/a	n/a
10	POLR2A	chr1:153518401-153518525	GM12878	blood:	n/a	n/a
11	MYC	chr1:153517306-153518676	NB4	blood:	n/a	n/a
12	SPI1	chr1:153517327-153518558	HL-60	blood:	n/a	n/a
13	POLR2A	chr1:153517252-153518703	HL-60	blood:	n/a	n/a
14	TCF12	chr1:153517295-153518597	A549	lung:	n/a	n/a
15	POLR2A	chr1:153517333-153518592	A549	lung:	n/a	n/a
16	POLR2A	chr1:153517166-153518620	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr1:153518400-153518550	AoAF	blood vessel:	n/a	n/a
18	CREB1	chr1:153517413-153518490	A549	lung:	n/a	n/a
19	EBF1	chr1:153518255-153518589	GM12878	blood:	n/a	chr1:153518437-153518448
20	MAX	chr1:153517358-153518572	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr1:153517217-153518582	Hela-S3	cervix:	n/a	n/a
22	GTF2F1	chr1:153517047-153518664	Hela-S3	cervix:	n/a	n/a
23	EP300	chr1:153517227-153518523	A549	lung:	n/a	n/a
24	POLR2A	chr1:153516836-153518740	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:153517331-153518557	A549	lung:	n/a	n/a
26	EBF1	chr1:153518048-153518606	GM12878	blood:	n/a	chr1:153518437-153518448 chr1:153518593-153518606
27	POLR2A	chr1:153517229-153518656	K562	blood:	n/a	n/a
28	MAZ	chr1:153517249-153519081	IMR90	lung:	n/a	n/a
29	CTCF	chr1:153518400-153518550	AG09319	gingival:	n/a	n/a
30	POLR2A	chr1:153516716-153518656	ProgFib	skin:	n/a	n/a
31	CTCF	chr1:153518400-153518550	AG10803	skin:	n/a	n/a
32	POLR2A	chr1:153518113-153518583	GM12892	blood:	n/a	n/a
33	POLR2A	chr1:153514113-153518626	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr1:153516714-153518750	HL-60	blood:	n/a	n/a
35	POLR2A	chr1:153517042-153518636	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr1:153517340-153518542	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr1:153518380-153518530	AG04449	skin:	n/a	n/a
38	MAX	chr1:153516656-153518729	A549	lung:	n/a	chr1:153517092-153517101
39	MAX	chr1:153516828-153518688	A549	lung:	n/a	chr1:153517092-153517101
40	JUND	chr1:153518115-153518637	A549	lung:	n/a	n/a
41	CTCF	chr1:153518400-153518550	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:153517112-153518622	A549	lung:	n/a	n/a
43	SMARCC1	chr1:153517009-153518647	Hela-S3	cervix:	n/a	n/a
44	MAX	chr1:153517324-153518694	NB4	blood:	n/a	n/a
45	POLR2A	chr1:153516654-153518595	HCT-116	colon:	n/a	n/a
46	TCF12	chr1:153516679-153519108	A549	lung:	n/a	n/a
47	MAX	chr1:153517374-153518623	Hela-S3	cervix:	n/a	n/a
48	CHD2	chr1:153518073-153518634	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:153516740-153518708	PBDE	blood:	n/a	n/a
50	TBP	chr1:153517381-153518532	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153518476-153518526	NHDF-neo	bronchial:	n/a
2	chr1:153518476-153518526	HUVEC	blood vessel:	n/a
3	chr1:153518476-153518526	HCT-116	colon:	n/a
4	chr1:153518476-153518526	SK-N-MC	brain:	n/a
5	chr1:153518476-153518526	SKMC	muscle:	n/a
6	chr1:153518476-153518526	LNCaP	prostate:	n/a
7	chr1:153518476-153518526	CMK	blood:	n/a
8	chr1:153518476-153518526	HEK293	kidney:	embryo
9	chr1:153518476-153518526	U87	brain:	n/a
10	chr1:153518476-153518526	A549	lung:	n/a
11	chr1:153518476-153518526	Hela-S3	cervix:	n/a
12	chr1:153518476-153518526	PANC-1	pancreas:	n/a
13	chr1:153518476-153518526	H1-hESC	embryonic stem cell:	embryo
14	chr1:153518476-153518526	AG04450	lung:	fetal
15	chr1:153518476-153518526	AoSMC	blood vessel:	n/a
16	chr1:153518476-153518526	ProgFib	skin:	n/a
17	chr1:153518476-153518526	IMR90	lung:	fetal
18	chr1:153518476-153518526	BJ	skin:	n/a
19	chr1:153518476-153518526	NH-A	brain:	n/a
20	chr1:153518476-153518526	NB4	blood:	n/a
21	chr1:153518476-153518526	PFSK-1	brain:	n/a
22	chr1:153518476-153518526	GM19239	blood:	n/a
23	chr1:153518476-153518526	HCPEpiC	choroid plexus:	n/a
24	chr1:153518476-153518526	SK-N-SH	brain:	n/a
25	chr1:153518476-153518526	Hepatocyte	liver:	n/a
26	chr1:153518476-153518526	HAEpiC	amniotic membrane:	n/a
27	chr1:153518476-153518526	GM12892	blood:	n/a
28	chr1:153518476-153518526	MCF10A-Er-Src	breast:	n/a
29	chr1:153518476-153518526	GM12878	blood:	n/a
30	chr1:153518476-153518526	HRE	kidney:	n/a
31	chr1:153518476-153518526	AG10803	skin:	n/a
32	chr1:153518476-153518526	GM06990	blood:	n/a
33	chr1:153518476-153518526	HNPCEpiC	eye:	n/a
34	chr1:153518476-153518526	AG09309	skin:	n/a
35	chr1:153518476-153518526	HIPEpiC	eye:	n/a
36	chr1:153518476-153518526	HepG2	liver:	n/a
37	chr1:153518476-153518526	Caco-2	colon:	n/a
38	chr1:153518476-153518526	SK-N-SH_RA	brain:	n/a
39	chr1:153518476-153518526	HCF	heart:	n/a
40	chr1:153518476-153518526	HL-60	blood:	n/a
41	chr1:153518476-153518526	ovcar-3	ovarian:	n/a
42	chr1:153518476-153518526	AG09319	gingival:	n/a
43	chr1:153518476-153518526	T-47D	breast:	n/a
44	chr1:153518476-153518526	HEEpiC	esophagus:	n/a
45	chr1:153518476-153518526	ECC-1	luminal epithelium:	n/a
46	chr1:153518476-153518526	GM12891	blood:	n/a
47	chr1:153518476-153518526	RPTEC	kidney:	n/a
48	chr1:153518476-153518526	Jurkat	blood:	n/a
49	chr1:153518476-153518526	K562	blood:	n/a
50	chr1:153518476-153518526	NHBE	bronchial:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr1:153507550..153508606-chr1:153517687..153518604,3	Hela-S3	cervix:
2	chr1:153517686..153519228-chr1:153538736..153541189,3	K562	blood:
3	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
4	chr1:153517525..153519027-chr1:153598182..153599900,2	K562	blood:
5	chr1:153517627..153518540-chr20:30194321..30195268,2	Hela-S3	cervix:
6	chr1:153508634..153510673-chr1:153516202..153519160,2	K562	blood:
7	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
8	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:
9	chr1:153327754..153330695-chr1:153517590..153520533,2	K562	blood:
10	chr1:153517755..153518567-chr17:62222638..62223343,2	HCT-116	colon:

No data

Variant related genes	Relation type
S100A5	TF binding region
S100A4	TF binding region
S100A4	CpG island
S100A5	CpG island
ENSG00000188643	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000266402	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	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11488669	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835437	0.91[EUR][1000 genomes]
rs16835455	0.91[EUR][1000 genomes]
rs1810765	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28452456	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28548347	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594230	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28689606	0.97[EUR][1000 genomes]
rs28718953	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36022742	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762268	0.94[EUR][1000 genomes]
rs41265160	0.96[AFR][1000 genomes]
rs41265162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595398	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55955983	0.94[EUR][1000 genomes]
rs56057245	0.84[EUR][1000 genomes]
rs56089062	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56350425	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56838169	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57024596	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58056804	0.97[EUR][1000 genomes]
rs58072118	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59376279	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60218214	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60287468	0.97[EUR][1000 genomes]
rs60969679	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61265945	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115473	0.97[EUR][1000 genomes]
rs74115476	0.91[EUR][1000 genomes]
rs743687	0.82[EUR][1000 genomes]
rs7535476	0.94[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:115 , 50 per page) page: 1 2 3

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	chr1:153515400-153518600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:153515400-153518600	Enhancers	Osteobl	bone
5	chr1:153515400-153522800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:153515400-153523000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:153515600-153518800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr1:153515600-153520000	Enhancers	HMEC	breast
9	chr1:153516200-153518600	Enhancers	Fetal Lung	lung
10	chr1:153516200-153520600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:153516400-153518600	Enhancers	Small Intestine	intestine
12	chr1:153516400-153518800	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr1:153516400-153519000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:153516600-153519000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr1:153516800-153518600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:153516800-153518600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:153516800-153518600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr1:153516800-153518600	Flanking Active TSS	Colonic Mucosa	Colon
19	chr1:153516800-153518600	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr1:153516800-153518600	Flanking Active TSS	Fetal Thymus	thymus
21	chr1:153516800-153518600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr1:153516800-153518600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr1:153516800-153518800	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr1:153516800-153518800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr1:153516800-153518800	Flanking Active TSS	Esophagus	oesophagus
26	chr1:153516800-153518800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr1:153516800-153519000	Enhancers	Fetal Intestine Large	intestine
28	chr1:153516800-153519200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr1:153516800-153519600	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr1:153516800-153520400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:153516800-153521800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:153516800-153522000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:153516800-153522400	Enhancers	Fetal Intestine Small	intestine
34	chr1:153517000-153518600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:153517000-153518600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:153517000-153518600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:153517000-153518600	Enhancers	Brain Substantia Nigra	brain
38	chr1:153517000-153518600	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:153517000-153518600	Flanking Active TSS	Placenta	Placenta
40	chr1:153517000-153518600	Flanking Active TSS	Left Ventricle	heart
41	chr1:153517000-153518600	Flanking Active TSS	HSMM	muscle
42	chr1:153517000-153518800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:153517000-153519000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr1:153517000-153519800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:153517000-153519800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:153517000-153519800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr1:153517200-153518600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr1:153517200-153518600	Flanking Active TSS	Lung	lung
49	chr1:153517200-153518800	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr1:153517200-153518800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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