Variant report

Variant	rs2028138
Chromosome Location	chr2:55459094-55459095
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:289)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:289 , 50 per page) page: 1 2 3 4 5 6

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	REST	chr2:55458997-55459547	K562	blood:	n/a	n/a
6	POLR2A	chr2:55458967-55461056	K562	blood:	n/a	n/a
7	SP1	chr2:55459014-55459970	H1-hESC	embryonic stem cell:	n/a	n/a
8	RUNX3	chr2:55458943-55460719	GM12878	blood:	n/a	n/a
9	TCF12	chr2:55458907-55460413	ECC-1	luminal epithelium:	n/a	n/a
10	YY1	chr2:55459022-55459577	ECC-1	luminal epithelium:	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	YY1	chr2:55458937-55460460	A549	lung:	n/a	chr2:55459829-55459849
14	POLR2A	chr2:55458934-55460788	U87	brain:	n/a	n/a
15	HEY1	chr2:55459065-55461114	K562	blood:	n/a	n/a
16	SMARCC1	chr2:55458745-55460606	Hela-S3	cervix:	n/a	chr2:55459487-55459496
17	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
18	MTA3	chr2:55458589-55461547	GM12878	blood:	n/a	n/a
19	HCFC1	chr2:55458624-55460325	K562	blood:	n/a	n/a
20	POLR2A	chr2:55458977-55460394	H1-neurons	neurons:	n/a	n/a
21	ELF1	chr2:55458502-55460607	HCT-116	colon:	n/a	chr2:55459306-55459319
22	SRF	chr2:55458647-55459625	ECC-1	luminal epithelium:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
23	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
24	POLR2A	chr2:55459010-55461927	HUVEC	blood vessel:	n/a	n/a
25	SP4	chr2:55459055-55460290	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr2:55458583-55460929	A549	lung:	n/a	n/a
27	EP300	chr2:55458841-55460139	A549	lung:	n/a	chr2:55459308-55459315
28	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
29	SIN3AK20	chr2:55458980-55460006	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr2:55458976-55460642	ProgFib	skin:	n/a	n/a
31	MAX	chr2:55458827-55460650	Hela-S3	cervix:	n/a	n/a
32	MAFK	chr2:55458993-55459997	Hela-S3	cervix:	n/a	chr2:55459207-55459221
33	POLR2A	chr2:55459082-55460051	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
37	MYBL2	chr2:55458767-55460463	HepG2	liver:	n/a	n/a
38	POLR2A	chr2:55459090-55460434	Gliobla	brain:	n/a	n/a
39	NFIC	chr2:55458975-55460435	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:55458854-55460349	HCT-116	colon:	n/a	n/a
41	PML	chr2:55458826-55460285	K562	blood:	n/a	n/a
42	SRF	chr2:55458454-55460313	HCT-116	colon:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
43	CEBPD	chr2:55458982-55459469	HepG2	liver:	n/a	n/a
44	ELF1	chr2:55458560-55460252	MCF-7	breast:	n/a	chr2:55459306-55459319
45	TCF12	chr2:55458935-55460152	ECC-1	luminal epithelium:	n/a	n/a
46	MBD4	chr2:55458795-55461839	HepG2	liver:	n/a	n/a
47	ELK1	chr2:55458622-55460326	K562	blood:	n/a	chr2:55459307-55459316 chr2:55459307-55459316
48	TCF7L2	chr2:55459034-55460456	Hela-S3	cervix:	n/a	n/a
49	ELF1	chr2:55458636-55459961	A549	lung:	n/a	chr2:55459306-55459319
50	WRNIP1	chr2:55458788-55461008	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:55459073-55459123	HCM	heart:	n/a
2	chr2:55459073-55459123	Jurkat	blood:	n/a
3	chr2:55459073-55459123	AG10803	skin:	n/a
4	chr2:55459073-55459123	HMEC	breast:	n/a
5	chr2:55459073-55459123	NB4	blood:	n/a
6	chr2:55459073-55459123	HCF	heart:	n/a
7	chr2:55459073-55459123	ProgFib	skin:	n/a
8	chr2:55459073-55459123	HUVEC	blood vessel:	n/a
9	chr2:55459073-55459123	MCF10A-Er-Src	breast:	n/a
10	chr2:55459073-55459123	SAEC	small airway:	n/a
11	chr2:55459073-55459123	HL-60	blood:	n/a
12	chr2:55459073-55459123	SK-N-MC	brain:	n/a
13	chr2:55459073-55459123	AG04450	lung:	fetal
14	chr2:55459073-55459123	SK-N-SH_RA	brain:	n/a
15	chr2:55459073-55459123	AG09319	gingival:	n/a
16	chr2:55459073-55459123	ECC-1	luminal epithelium:	n/a
17	chr2:55459073-55459123	HepG2	liver:	n/a
18	chr2:55459073-55459123	PANC-1	pancreas:	n/a
19	chr2:55459073-55459123	SKMC	muscle:	n/a
20	chr2:55459073-55459123	LNCaP	prostate:	n/a
21	chr2:55459073-55459123	Hepatocyte	liver:	n/a
22	chr2:55459073-55459123	HCT-116	colon:	n/a
23	chr2:55459073-55459123	HRCEpiC	kidney:	n/a
24	chr2:55459073-55459123	PrEC	prostate:	n/a
25	chr2:55459073-55459123	HCPEpiC	choroid plexus:	n/a
26	chr2:55459073-55459123	NHDF-neo	bronchial:	n/a
27	chr2:55459073-55459123	IMR90	lung:	fetal
28	chr2:55459073-55459123	PFSK-1	brain:	n/a
29	chr2:55459073-55459123	Hela-S3	cervix:	n/a
30	chr2:55459073-55459123	RPTEC	kidney:	n/a
31	chr2:55459073-55459123	GM19239	blood:	n/a
32	chr2:55459073-55459123	GM12878	blood:	n/a
33	chr2:55459073-55459123	GM06990	blood:	n/a
34	chr2:55459073-55459123	NH-A	brain:	n/a
35	chr2:55459073-55459123	GM12892	blood:	n/a
36	chr2:55459073-55459123	HRE	kidney:	n/a
37	chr2:55459073-55459123	BJ	skin:	n/a
38	chr2:55459073-55459123	BE2_C	brain:	n/a
39	chr2:55459073-55459123	AoSMC	blood vessel:	n/a
40	chr2:55459073-55459123	HRPEpiC	eye:	n/a
41	chr2:55459073-55459123	HIPEpiC	eye:	n/a
42	chr2:55459073-55459123	MCF-7	breast:	n/a
43	chr2:55459073-55459123	HEK293	kidney:	embryo
44	chr2:55459073-55459123	K562	blood:	n/a
45	chr2:55459073-55459123	T-47D	breast:	n/a
46	chr2:55459073-55459123	NHBE	bronchial:	n/a
47	chr2:55459073-55459123	H1-hESC	embryonic stem cell:	embryo
48	chr2:55459073-55459123	Caco-2	colon:	n/a
49	chr2:55459073-55459123	NT2-D1	testis:	n/a
50	chr2:55459073-55459123	CMK	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
2	chr12:110338094..110338823-chr2:55458974..55459662,2	Hela-S3	cervix:
3	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
4	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
5	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
6	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
7	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
8	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
9	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
10	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:

No data

Variant related genes	Relation type
RPS27A	TF binding region
RPS27A	CpG island
ENSG00000138041	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000139437	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10176839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183953	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10439479	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11694920	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12464094	0.86[EUR][1000 genomes]
rs12713290	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1437389	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1437392	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043714	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2118283	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2164715	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2576723	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589081	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589082	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589083	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589097	0.87[EUR][1000 genomes]
rs2589098	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2920845	0.86[EUR][1000 genomes]
rs2920846	0.83[EUR][1000 genomes]
rs2920869	0.86[EUR][1000 genomes]
rs4233959	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4591380	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545476	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545479	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545482	0.84[EUR][1000 genomes]
rs6713058	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6715694	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6716066	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719579	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6723870	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747682	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6750501	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6754605	0.87[AMR][1000 genomes];0.85[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	chr2:55457800-55460000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:55457800-55460400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:55457800-55460400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:55458000-55460200	Active TSS	A549	lung
5	chr2:55458000-55460400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:55458200-55460000	Active TSS	K562	blood
7	chr2:55458200-55460200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:55458200-55460400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:55458200-55460600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:55458200-55460800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:55458200-55460800	Active TSS	HMEC	breast
12	chr2:55458400-55459200	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr2:55458400-55459200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr2:55458400-55459200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr2:55458400-55459400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:55458400-55459400	Flanking Active TSS	Liver	Liver
17	chr2:55458400-55459800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr2:55458400-55460200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:55458400-55460200	Active TSS	Stomach Smooth Muscle	stomach
20	chr2:55458400-55460400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr2:55458400-55460400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:55458400-55460400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:55458400-55460400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:55458400-55460600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr2:55458400-55460600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:55458400-55460600	Active TSS	Aorta	Aorta
27	chr2:55458400-55460600	Active TSS	Fetal Stomach	stomach
28	chr2:55458400-55460600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr2:55458400-55460600	Active TSS	Right Atrium	heart
30	chr2:55458400-55460600	Active TSS	GM12878-XiMat	blood
31	chr2:55458400-55460600	Active TSS	HSMM	muscle
32	chr2:55458400-55460600	Active TSS	NH-A	brain
33	chr2:55458400-55460600	Active TSS	NHLF	lung
34	chr2:55458400-55460800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:55458400-55460800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr2:55458400-55460800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:55458400-55460800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:55458400-55460800	Active TSS	Fetal Kidney	kidney
39	chr2:55458400-55460800	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr2:55458400-55461400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:55458600-55459200	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr2:55458600-55459200	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr2:55458600-55459200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:55458600-55459200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr2:55458600-55459200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:55458600-55459200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr2:55458600-55459200	Active TSS	Fetal Brain Male	brain
48	chr2:55458600-55459200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr2:55458600-55459200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr2:55458600-55460000	Active TSS	HUES64 Cell Line	embryonic stem cell

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