Variant report

Variant	rs749221
Chromosome Location	chr2:55496830-55496831
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:71)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:71 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55495499-55496934	PFSK-1	brain:	n/a	n/a
2	GABPA	chr2:55495609-55496835	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr2:55495566-55496917	GM12878	blood:	n/a	n/a
4	IRF1	chr2:55495850-55497084	K562	blood:	n/a	chr2:55496048-55496057 chr2:55497054-55497064 chr2:55497052-55497063 chr2:55497053-55497065
5	SIN3AK20	chr2:55495532-55496909	MCF-7	breast:	n/a	n/a
6	POLR2A	chr2:55495522-55497897	HepG2	liver:	n/a	n/a
7	UBTF	chr2:55495574-55497012	K562	blood:	n/a	n/a
8	ZNF384	chr2:55496131-55497051	GM12878	blood:	n/a	n/a
9	GTF2F1	chr2:55495902-55496932	Hela-S3	cervix:	n/a	n/a
10	MYC	chr2:55495397-55497273	A549	lung:	n/a	n/a
11	KAP1	chr2:55496112-55496920	U2OS	brain:	n/a	n/a
12	HA-E2F1	chr2:55495893-55496833	MCF-7	breast:	n/a	n/a
13	POLR2A	chr2:55495639-55497273	Raji	blood:	n/a	n/a
14	GABPA	chr2:55495386-55497058	A549	lung:	n/a	n/a
15	POLR2A	chr2:55495551-55496864	HUVEC	blood vessel:	n/a	n/a
16	MYC	chr2:55495871-55496943	Hela-S3	cervix:	n/a	n/a
17	MYBL2	chr2:55495437-55497054	HepG2	liver:	n/a	n/a
18	GATA3	chr2:55495947-55496853	MCF-7	breast:	n/a	n/a
19	POLR2A	chr2:55495599-55497066	Hela-S3	cervix:	n/a	n/a
20	MAX	chr2:55495624-55496861	HCT-116	colon:	n/a	n/a
21	POLR2A	chr2:55495696-55497121	PFSK-1	brain:	n/a	n/a
22	JUND	chr2:55495761-55496948	K562	blood:	n/a	chr2:55496869-55496878
23	TAF1	chr2:55495815-55496870	ECC-1	luminal epithelium:	n/a	n/a
24	RELA	chr2:55495940-55497076	GM15510	blood:	n/a	n/a
25	SRF	chr2:55495911-55496840	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:55495702-55497072	GM18505	blood:	n/a	n/a
27	IRF3	chr2:55496227-55496935	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:55495510-55497085	MCF10A-Er-Src	breast:	n/a	n/a
29	ATF2	chr2:55496025-55496883	GM12878	blood:	n/a	n/a
30	POLR2A	chr2:55495739-55497136	PBDE	blood:	n/a	n/a
31	ZNF274	chr2:55496746-55497153	K562	blood:	n/a	n/a
32	POLR2A	chr2:55495384-55496972	MCF10A-Er-Src	breast:	n/a	n/a
33	GABPA	chr2:55495600-55496839	SK-N-SH	brain:	n/a	n/a
34	SIN3AK20	chr2:55495710-55496834	HCT-116	colon:	n/a	n/a
35	MYC	chr2:55495809-55497111	K562	blood:	n/a	n/a
36	MYBL2	chr2:55495610-55497191	HepG2	liver:	n/a	n/a
37	HCFC1	chr2:55495537-55497147	Hela-S3	cervix:	n/a	n/a
38	NFIC	chr2:55496111-55496996	GM12878	blood:	n/a	n/a
39	TAF1	chr2:55495658-55497067	A549	lung:	n/a	n/a
40	ELF1	chr2:55495810-55496845	HCT-116	colon:	n/a	n/a
41	TEAD4	chr2:55495658-55496842	K562	blood:	n/a	n/a
42	BCL3	chr2:55495902-55496848	A549	lung:	n/a	chr2:55496096-55496109
43	RELA	chr2:55495776-55496970	GM19099	blood:	n/a	n/a
44	GABPA	chr2:55495645-55496900	HL-60	blood:	n/a	n/a
45	POLR2A	chr2:55495464-55497239	GM12891	blood:	n/a	n/a
46	GABPA	chr2:55495524-55496983	A549	lung:	n/a	n/a
47	STAT3	chr2:55496800-55496914	MCF10A-Er-Src	breast:	n/a	chr2:55496859-55496873
48	STAT5A	chr2:55495931-55497053	GM12878	blood:	n/a	chr2:55496859-55496873 chr2:55496428-55496448
49	SRF	chr2:55495862-55496851	HCT-116	colon:	n/a	n/a
50	POLR2A	chr2:55495487-55496904	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
2	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
3	chr2:55496544..55498355-chr2:55643954..55646229,2	K562	blood:
4	chr2:55274992..55277411-chr2:55494676..55497816,3	K562	blood:
5	chr2:55496311..55498089-chr2:55508225..55509799,2	MCF-7	breast:
6	chr2:55494928..55498059-chr2:55506695..55512310,8	K562	blood:
7	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
8	chr2:55496021..55497900-chr2:55843389..55845266,2	K562	blood:
9	chr2:55496021..55498315-chr2:55843389..55845953,2	K562	blood:
10	chr2:55475194..55477770-chr2:55494963..55497132,2	MCF-7	breast:
11	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
12	chr2:55494631..55497013-chr2:55842868..55845390,2	MCF-7	breast:

No data

Variant related genes	Relation type
MTIF2	TF binding region
ENSG00000085760	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10496041	1.00[CEU][hapmap]
rs11892007	1.00[CEU][hapmap]
rs12104902	1.00[CEU][hapmap]
rs12105731	1.00[CEU][hapmap]
rs1437387	1.00[CEU][hapmap]
rs1437388	1.00[CEU][hapmap]
rs17046793	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17046834	1.00[CEU][hapmap]
rs57055480	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58533450	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58560357	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60941520	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714576	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6726732	1.00[CEU][hapmap]
rs6727964	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6733567	1.00[CEU][hapmap]
rs9784090	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55494800-55497000	Active TSS	GM12878-XiMat	blood
2	chr2:55495200-55497000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:55495200-55497000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:55495200-55497200	Active TSS	Psoas Muscle	Psoas
5	chr2:55495400-55497000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:55495400-55497000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr2:55495400-55497000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:55495400-55497000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:55495400-55497000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:55495400-55497000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:55495400-55497000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr2:55495400-55497000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr2:55495400-55497000	Active TSS	Right Atrium	heart
14	chr2:55495400-55497000	Active TSS	Right Ventricle	heart
15	chr2:55495400-55497000	Active TSS	HSMM	muscle
16	chr2:55495400-55497200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr2:55495400-55497200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:55495400-55497200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr2:55495400-55497200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr2:55495400-55497200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:55495400-55497200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:55495400-55497200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:55495400-55497200	Active TSS	Fetal Muscle Trunk	muscle
24	chr2:55495400-55497200	Active TSS	Fetal Thymus	thymus
25	chr2:55495400-55497200	Active TSS	NHLF	lung
26	chr2:55495400-55497400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:55495600-55497000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr2:55495600-55497000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:55495600-55497000	Active TSS	Esophagus	oesophagus
30	chr2:55495600-55497000	Active TSS	Placenta	Placenta
31	chr2:55495600-55497000	Active TSS	Gastric	stomach
32	chr2:55495600-55497000	Active TSS	Lung	lung
33	chr2:55495600-55497000	Active TSS	Pancreas	Pancrea
34	chr2:55495600-55497000	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr2:55495600-55497000	Active TSS	Stomach Mucosa	stomach
36	chr2:55495600-55497200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:55495600-55497200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr2:55495600-55497200	Active TSS	Ovary	ovary
39	chr2:55495600-55497400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr2:55495800-55497000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr2:55495800-55497000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:55495800-55497000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr2:55495800-55497000	Active TSS	Fetal Stomach	stomach
44	chr2:55495800-55497000	Active TSS	Small Intestine	intestine
45	chr2:55495800-55497200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:55495800-55497200	Active TSS	Thymus	Thymus
47	chr2:55496000-55497000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:55496000-55497000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr2:55496000-55497000	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr2:55496000-55497000	Active TSS	Fetal Brain Female	brain

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