Variant report

Variant	rs2576723
Chromosome Location	chr2:55461570-55461571
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:63)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:63 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55458744-55464800	K562	blood:	n/a	n/a
2	POLR2A	chr2:55458959-55464692	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
4	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
5	POLR2A	chr2:55459010-55461927	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
7	POLR2A	chr2:55461391-55461690	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:55461342-55461654	HCT-116	colon:	n/a	n/a
12	MBD4	chr2:55458795-55461839	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:55461377-55461707	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:55461373-55464681	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:55459164-55464717	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:55458775-55464779	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr2:55458974-55464629	K562	blood:	n/a	n/a
18	POLR2A	chr2:55461349-55461736	GM12891	blood:	n/a	n/a
19	POLR2A	chr2:55461401-55461621	A549	lung:	n/a	n/a
20	POLR2A	chr2:55458908-55461808	K562	blood:	n/a	n/a
21	POLR2A	chr2:55458800-55464614	K562	blood:	n/a	n/a
22	POLR2A	chr2:55461372-55461659	A549	lung:	n/a	n/a
23	POLR2A	chr2:55461409-55461633	A549	lung:	n/a	n/a
24	POLR2A	chr2:55458988-55464662	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:55461421-55462031	U87	brain:	n/a	n/a
26	POLR2A	chr2:55461469-55464573	K562	blood:	n/a	n/a
27	POLR2A	chr2:55458860-55465354	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr2:55458989-55464724	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr2:55458966-55464603	GM12892	blood:	n/a	n/a
30	POLR2A	chr2:55460894-55461689	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:55459024-55464715	GM18505	blood:	n/a	n/a
32	ZNF263	chr2:55459016-55461900	HEK293-T-REx	kidney:	n/a	n/a
33	POLR2A	chr2:55458733-55465490	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr2:55458865-55465521	MCF-7	breast:	n/a	n/a
35	POLR2A	chr2:55460323-55464639	A549	lung:	n/a	n/a
36	POLR2A	chr2:55458817-55464677	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:55461565-55464760	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr2:55458685-55467019	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr2:55459009-55464639	GM12892	blood:	n/a	n/a
40	POLR2A	chr2:55459696-55465435	K562	blood:	n/a	n/a
41	POLR2A	chr2:55461263-55461827	HL-60	blood:	n/a	n/a
42	POLR2A	chr2:55458747-55464854	U87	brain:	n/a	n/a
43	POLR2A	chr2:55461332-55462156	GM12891	blood:	n/a	n/a
44	POLR2A	chr2:55461322-55461778	K562	blood:	n/a	n/a
45	POLR2A	chr2:55460860-55462031	U87	brain:	n/a	n/a
46	ATF2	chr2:55461348-55461866	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr2:55458947-55464599	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr2:55461354-55464525	GM12891	blood:	n/a	n/a
49	POLR2A	chr2:55461471-55461791	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr2:55461377-55461671	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:109618339..109619263-chr2:55460673..55461600,2	Hela-S3	cervix:
2	chr2:55459912..55461600-chr2:55842449..55844888,2	K562	blood:
3	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
4	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
5	chr17:57919487..57921628-chr2:55460501..55462131,2	MCF-7	breast:
6	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
7	chr2:55461063..55464036-chr2:55678930..55681673,2	MCF-7	breast:
8	chr2:55313997..55316994-chr2:55461231..55462844,2	K562	blood:

No data

Variant related genes	Relation type
CLHC1	TF binding region
ENSG00000138041	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000197780	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10176839	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10183953	0.84[EUR][1000 genomes]
rs10439479	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11694920	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12713290	0.84[EUR][1000 genomes]
rs1437389	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1437392	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1561231	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1561232	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1561233	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028138	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2043714	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2118283	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2164715	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589097	0.97[EUR][1000 genomes]
rs2589098	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589099	0.89[ASN][1000 genomes]
rs4233959	0.84[EUR][1000 genomes]
rs4591380	0.84[EUR][1000 genomes]
rs6545476	0.84[EUR][1000 genomes]
rs6545479	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6545482	1.00[EUR][1000 genomes]
rs6713058	0.84[EUR][1000 genomes]
rs6715694	0.84[EUR][1000 genomes]
rs6716066	0.84[EUR][1000 genomes]
rs6719579	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6723870	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6747682	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6750501	0.84[EUR][1000 genomes]
rs6754605	1.00[AMR][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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55458600-55462200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:55459200-55461600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:55459800-55461800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
4	chr2:55459800-55462000	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr2:55460000-55462400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
6	chr2:55460000-55463000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
7	chr2:55460000-55463400	Transcr. at gene 5' and 3'	K562	blood
8	chr2:55460200-55462000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
9	chr2:55460200-55462200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55460200-55462600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr2:55460200-55463000	Transcr. at gene 5' and 3'	A549	lung
12	chr2:55460400-55461600	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:55460400-55461800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
14	chr2:55460400-55461800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:55460400-55461800	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:55460400-55461800	Transcr. at gene 5' and 3'	NHEK	skin
17	chr2:55460400-55462000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
18	chr2:55460400-55462000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:55460400-55462400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
20	chr2:55460400-55462400	Transcr. at gene 5' and 3'	Hela-S3	cervix
21	chr2:55460400-55462600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
22	chr2:55460400-55462600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:55460400-55463000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:55460600-55461600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:55460600-55461600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
26	chr2:55460600-55461600	Transcr. at gene 5' and 3'	HSMM	muscle
27	chr2:55460600-55461800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
28	chr2:55460600-55461800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:55460600-55461800	Transcr. at gene 5' and 3'	NHLF	lung
30	chr2:55460600-55462000	Transcr. at gene 5' and 3'	Osteobl	bone
31	chr2:55460600-55462200	Transcr. at gene 5' and 3'	NH-A	brain
32	chr2:55460600-55462400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
33	chr2:55460600-55462600	Weak transcription	Aorta	Aorta
34	chr2:55460600-55463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:55460600-55463800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr2:55460800-55461600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:55460800-55461800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:55460800-55461800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
39	chr2:55460800-55462000	Transcr. at gene 5' and 3'	HMEC	breast
40	chr2:55460800-55462200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:55460800-55462600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
42	chr2:55460800-55462600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
43	chr2:55461000-55461600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:55461000-55461600	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:55461000-55461600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:55461000-55461600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:55461000-55461600	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
48	chr2:55461000-55461600	Genic enhancers	Fetal Muscle Leg	muscle
49	chr2:55461000-55461600	Genic enhancers	Placenta	Placenta
50	chr2:55461000-55461600	Genic enhancers	Fetal Thymus	thymus

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