Variant report

Variant	rs2028139
Chromosome Location	chr2:55460017-55460018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:385)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:385 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55458996-55460836	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:55458744-55464800	K562	blood:	n/a	n/a
3	ELF1	chr2:55458669-55460096	A549	lung:	n/a	chr2:55459306-55459319
4	CEBPB	chr2:55459053-55460191	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:55459565-55460618	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:55458967-55461056	K562	blood:	n/a	n/a
7	RUNX3	chr2:55458943-55460719	GM12878	blood:	n/a	n/a
8	TCF12	chr2:55458907-55460413	ECC-1	luminal epithelium:	n/a	n/a
9	RELA	chr2:55459328-55460378	GM12892	blood:	n/a	n/a
10	MYC	chr2:55459255-55460629	K562	blood:	n/a	n/a
11	POLR2A	chr2:55458959-55464692	GM12878	blood:	n/a	n/a
12	CHD2	chr2:55458909-55460030	H1-hESC	embryonic stem cell:	n/a	n/a
13	UBTF	chr2:55459671-55460474	K562	blood:	n/a	n/a
14	YY1	chr2:55459596-55460020	K562	blood:	n/a	chr2:55459829-55459849
15	YY1	chr2:55458937-55460460	A549	lung:	n/a	chr2:55459829-55459849
16	POLR2A	chr2:55458934-55460788	U87	brain:	n/a	n/a
17	HEY1	chr2:55459065-55461114	K562	blood:	n/a	n/a
18	SMARCC1	chr2:55458745-55460606	Hela-S3	cervix:	n/a	chr2:55459487-55459496
19	ZKSCAN1	chr2:55459125-55460469	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
21	MTA3	chr2:55458589-55461547	GM12878	blood:	n/a	n/a
22	MYC	chr2:55459245-55460439	K562	blood:	n/a	n/a
23	HCFC1	chr2:55458624-55460325	K562	blood:	n/a	n/a
24	POLR2A	chr2:55458977-55460394	H1-neurons	neurons:	n/a	n/a
25	ELF1	chr2:55458502-55460607	HCT-116	colon:	n/a	chr2:55459306-55459319
26	TBP	chr2:55459098-55460493	GM12878	blood:	n/a	n/a
27	MAX	chr2:55459161-55460475	H1-hESC	embryonic stem cell:	n/a	n/a
28	GTF2F1	chr2:55459122-55460114	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
30	POLR2A	chr2:55459010-55461927	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr2:55459152-55460219	K562	blood:	n/a	n/a
32	SP4	chr2:55459055-55460290	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr2:55458583-55460929	A549	lung:	n/a	n/a
34	EP300	chr2:55458841-55460139	A549	lung:	n/a	chr2:55459308-55459315
35	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
36	POLR2A	chr2:55458976-55460642	ProgFib	skin:	n/a	n/a
37	MAX	chr2:55458827-55460650	Hela-S3	cervix:	n/a	n/a
38	ELF1	chr2:55459193-55460069	SK-N-SH	brain:	n/a	chr2:55459306-55459319
39	MYC	chr2:55460017-55460021	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr2:55459082-55460051	HepG2	liver:	n/a	n/a
41	TAF1	chr2:55459572-55460022	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr2:55459133-55460068	IMR90	lung:	n/a	n/a
44	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
46	MYBL2	chr2:55458767-55460463	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:55459090-55460434	Gliobla	brain:	n/a	n/a
48	NFIC	chr2:55458975-55460435	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:55458854-55460349	HCT-116	colon:	n/a	n/a
50	PML	chr2:55458826-55460285	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:55460012-55460062	MCF-7	breast:	n/a
2	chr2:55460012-55460062	PFSK-1	brain:	n/a
3	chr2:55460012-55460062	AG09319	gingival:	n/a
4	chr2:55460012-55460062	ovcar-3	ovarian:	n/a
5	chr2:55460012-55460062	HMEC	breast:	n/a
6	chr2:55460012-55460062	ECC-1	luminal epithelium:	n/a
7	chr2:55460012-55460062	NHDF-neo	bronchial:	n/a
8	chr2:55460012-55460062	AG04449	skin:	fetal
9	chr2:55460012-55460062	NH-A	brain:	n/a
10	chr2:55460012-55460062	HAEpiC	amniotic membrane:	n/a
11	chr2:55460012-55460062	Hela-S3	cervix:	n/a
12	chr2:55460012-55460062	BE2_C	brain:	n/a
13	chr2:55460012-55460062	HRE	kidney:	n/a
14	chr2:55460012-55460062	GM19239	blood:	n/a
15	chr2:55460012-55460062	PANC-1	pancreas:	n/a
16	chr2:55460012-55460062	AG10803	skin:	n/a
17	chr2:55460012-55460062	NT2-D1	testis:	n/a
18	chr2:55460012-55460062	HepG2	liver:	n/a
19	chr2:55460012-55460062	H1-hESC	embryonic stem cell:	embryo
20	chr2:55460012-55460062	K562	blood:	n/a
21	chr2:55460012-55460062	LNCaP	prostate:	n/a
22	chr2:55460012-55460062	BJ	skin:	n/a
23	chr2:55460012-55460062	HEEpiC	esophagus:	n/a
24	chr2:55460012-55460062	HRPEpiC	eye:	n/a
25	chr2:55460012-55460062	AG04450	lung:	fetal
26	chr2:55460012-55460062	HCPEpiC	choroid plexus:	n/a
27	chr2:55460012-55460062	AoSMC	blood vessel:	n/a
28	chr2:55460012-55460062	SKMC	muscle:	n/a
29	chr2:55460012-55460062	HIPEpiC	eye:	n/a
30	chr2:55460012-55460062	SAEC	small airway:	n/a
31	chr2:55460012-55460062	Caco-2	colon:	n/a
32	chr2:55460012-55460062	HNPCEpiC	eye:	n/a
33	chr2:55460012-55460062	MCF10A-Er-Src	breast:	n/a
34	chr2:55460012-55460062	SK-N-SH_RA	brain:	n/a
35	chr2:55460012-55460062	U87	brain:	n/a
36	chr2:55460012-55460062	HCM	heart:	n/a
37	chr2:55460012-55460062	Hepatocyte	liver:	n/a
38	chr2:55460012-55460062	A549	lung:	n/a
39	chr2:55460012-55460062	AG09309	skin:	n/a
40	chr2:55460012-55460062	GM12891	blood:	n/a
41	chr2:55460012-55460062	ProgFib	skin:	n/a
42	chr2:55460012-55460062	HCF	heart:	n/a
43	chr2:55460012-55460062	PrEC	prostate:	n/a
44	chr2:55460012-55460062	Jurkat	blood:	n/a
45	chr2:55460012-55460062	IMR90	lung:	fetal
46	chr2:55460012-55460062	CMK	blood:	n/a
47	chr2:55460012-55460062	NB4	blood:	n/a
48	chr2:55460012-55460062	GM06990	blood:	n/a
49	chr2:55460012-55460062	HCT-116	colon:	n/a
50	chr2:55460012-55460062	HPAEpiC	pulmonary alveolar:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
2	chr2:55459243..55461012-chr2:55645151..55647509,2	MCF-7	breast:
3	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
4	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
5	chr2:55459912..55461600-chr2:55842449..55844888,2	K562	blood:
6	chr2:55275729..55276355-chr2:55459417..55460280,3	Hela-S3	cervix:
7	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
8	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
9	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
10	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
11	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
12	chr12:10765822..10766366-chr2:55459151..55460039,2	HCT-116	colon:
13	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
14	chr16:67207875..67208482-chr2:55459236..55460116,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
CLHC1	TF binding region
RPS27A	TF binding region
RPS27A	CpG island
CLHC1	CpG island
ENSG00000162997	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000111196	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000140939	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10496038	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs1134722	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11686766	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs11686912	0.89[CEU][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs11687876	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12989854	0.86[EUR][1000 genomes]
rs12995548	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs13000786	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13003020	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13012567	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13014752	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017468	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13032294	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs34447956	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35141050	0.86[EUR][1000 genomes]
rs35183885	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35227659	0.86[EUR][1000 genomes]
rs35700883	0.86[EUR][1000 genomes]
rs36121000	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4318424	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs4627623	0.92[AMR][1000 genomes]
rs6742306	0.89[CEU][hapmap];0.82[YRI][hapmap];0.94[EUR][1000 genomes]
rs6743339	0.89[EUR][1000 genomes]
rs6747466	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs71414544	0.86[EUR][1000 genomes]
rs71414545	0.86[EUR][1000 genomes]
rs71414546	0.86[EUR][1000 genomes]
rs71414547	0.86[EUR][1000 genomes]
rs71414548	0.86[EUR][1000 genomes]
rs71414549	0.84[EUR][1000 genomes]
rs71414556	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71414557	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55457800-55460400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:55457800-55460400	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr2:55458000-55460200	Active TSS	A549	lung
4	chr2:55458000-55460400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:55458200-55460200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:55458200-55460400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:55458200-55460600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:55458200-55460800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:55458200-55460800	Active TSS	HMEC	breast
10	chr2:55458400-55460200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr2:55458400-55460200	Active TSS	Stomach Smooth Muscle	stomach
12	chr2:55458400-55460400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr2:55458400-55460400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr2:55458400-55460400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55458400-55460400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:55458400-55460600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr2:55458400-55460600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:55458400-55460600	Active TSS	Aorta	Aorta
19	chr2:55458400-55460600	Active TSS	Fetal Stomach	stomach
20	chr2:55458400-55460600	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:55458400-55460600	Active TSS	Right Atrium	heart
22	chr2:55458400-55460600	Active TSS	GM12878-XiMat	blood
23	chr2:55458400-55460600	Active TSS	HSMM	muscle
24	chr2:55458400-55460600	Active TSS	NH-A	brain
25	chr2:55458400-55460600	Active TSS	NHLF	lung
26	chr2:55458400-55460800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:55458400-55460800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr2:55458400-55460800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:55458400-55460800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:55458400-55460800	Active TSS	Fetal Kidney	kidney
31	chr2:55458400-55460800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr2:55458400-55461400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:55458600-55460200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:55458600-55460200	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr2:55458600-55460400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:55458600-55460400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:55458600-55460400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:55458600-55460400	Active TSS	Muscle Satellite Cultured Cells	--
39	chr2:55458600-55460400	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:55458600-55460400	Active TSS	Colonic Mucosa	Colon
41	chr2:55458600-55460400	Active TSS	Hela-S3	cervix
42	chr2:55458600-55460400	Active TSS	NHEK	skin
43	chr2:55458600-55460600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr2:55458600-55460600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:55458600-55460600	Active TSS	Fetal Muscle Trunk	muscle
46	chr2:55458600-55460600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr2:55458600-55460600	Active TSS	Small Intestine	intestine
48	chr2:55458600-55460600	Active TSS	Thymus	Thymus
49	chr2:55458600-55460800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:55458600-55460800	Active TSS	Fetal Intestine Large	intestine

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