Variant report

Variant	rs553400040
Chromosome Location	chr3:48957290-48957291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:174)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:174 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48957004-48957524	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:48955622-48957513	K562	blood:	n/a	n/a
3	CHD1	chr3:48955533-48957765	IMR90	lung:	n/a	n/a
4	POLR2A	chr3:48956891-48957429	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:48957149-48957446	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:48957122-48957507	GM12891	blood:	n/a	n/a
7	IRF1	chr3:48957003-48957457	K562	blood:	n/a	n/a
8	SIN3AK20	chr3:48957215-48957474	PFSK-1	brain:	n/a	n/a
9	HCFC1	chr3:48955446-48957694	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:48955591-48957632	HUVEC	blood vessel:	n/a	n/a
11	USF1	chr3:48957230-48957521	HepG2	liver:	n/a	chr3:48957380-48957391
12	TAF1	chr3:48957190-48957511	Hela-S3	cervix:	n/a	n/a
13	USF1	chr3:48957215-48957537	SK-N-SH_RA	brain:	n/a	chr3:48957380-48957391
14	POLR2A	chr3:48955395-48957740	GM12878	blood:	n/a	n/a
15	MXI1	chr3:48955627-48957576	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:48957254-48957379	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:48957182-48957702	HL-60	blood:	n/a	n/a
18	GATA1	chr3:48955593-48957469	PBDE	blood:	n/a	n/a
19	MAX	chr3:48955611-48957523	GM12878	blood:	n/a	chr3:48957381-48957391
20	MAX	chr3:48956246-48957446	A549	lung:	n/a	chr3:48957381-48957391
21	USF1	chr3:48956763-48957655	HCT-116	colon:	n/a	chr3:48957380-48957391
22	POLR2A	chr3:48955558-48957494	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:48955479-48957684	Hela-S3	cervix:	n/a	n/a
24	USF1	chr3:48957233-48957522	A549	lung:	n/a	chr3:48957380-48957391
25	HEY1	chr3:48957111-48957533	HepG2	liver:	n/a	n/a
26	TBP	chr3:48957200-48957500	HepG2	liver:	n/a	n/a
27	PML	chr3:48955461-48957615	GM12878	blood:	n/a	n/a
28	YY1	chr3:48957243-48957527	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:48957119-48957558	PANC-1	pancreas:	n/a	n/a
30	TBP	chr3:48957073-48957471	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr3:48957230-48957437	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:48957145-48957473	HCT-116	colon:	n/a	n/a
33	POLR2A	chr3:48956652-48957585	GM12892	blood:	n/a	n/a
34	POLR2A	chr3:48956983-48957615	GM12892	blood:	n/a	n/a
35	MAX	chr3:48955575-48957609	K562	blood:	n/a	chr3:48957381-48957391
36	SIN3AK20	chr3:48957224-48957488	HepG2	liver:	n/a	n/a
37	MAX	chr3:48955477-48957761	HepG2	liver:	n/a	chr3:48957381-48957391
38	ATF2	chr3:48956958-48957507	GM12878	blood:	n/a	n/a
39	SMC3	chr3:48956605-48957505	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:48957029-48957549	K562	blood:	n/a	n/a
41	MXI1	chr3:48955445-48957924	SK-N-SH	brain:	n/a	n/a
42	USF1	chr3:48957231-48957477	HepG2	liver:	n/a	chr3:48957380-48957391
43	POLR2A	chr3:48956812-48957574	GM12891	blood:	n/a	n/a
44	EBF1	chr3:48957226-48957387	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:48957110-48957542	GM12892	blood:	n/a	n/a
46	POLR2A	chr3:48957245-48957489	ECC-1	luminal epithelium:	n/a	n/a
47	USF1	chr3:48957147-48957604	SK-N-SH	brain:	n/a	chr3:48957380-48957391
48	JUND	chr3:48957246-48957483	K562	blood:	n/a	n/a
49	CHD1	chr3:48956816-48957387	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:48957192-48957470	HCT-116	colon:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48957246-48957296	MCF-7	breast:	n/a
2	chr3:48957246-48957296	HEEpiC	esophagus:	n/a
3	chr3:48957246-48957296	ECC-1	luminal epithelium:	n/a
4	chr3:48957246-48957296	GM12892	blood:	n/a
5	chr3:48957246-48957296	HUVEC	blood vessel:	n/a
6	chr3:48957246-48957296	HMEC	breast:	n/a
7	chr3:48957246-48957296	AoSMC	blood vessel:	n/a
8	chr3:48957246-48957296	AG04450	lung:	fetal
9	chr3:48957246-48957296	HCM	heart:	n/a
10	chr3:48957246-48957296	H1-hESC	embryonic stem cell:	embryo
11	chr3:48957246-48957296	HRPEpiC	eye:	n/a
12	chr3:48957246-48957296	HIPEpiC	eye:	n/a
13	chr3:48957246-48957296	PrEC	prostate:	n/a
14	chr3:48957246-48957296	IMR90	lung:	fetal
15	chr3:48957246-48957296	HepG2	liver:	n/a
16	chr3:48957246-48957296	SK-N-SH	brain:	n/a
17	chr3:48957246-48957296	HNPCEpiC	eye:	n/a
18	chr3:48957246-48957296	HRE	kidney:	n/a
19	chr3:48957246-48957296	HEK293	kidney:	embryo
20	chr3:48957246-48957296	ovcar-3	ovarian:	n/a
21	chr3:48957246-48957296	HL-60	blood:	n/a
22	chr3:48957246-48957296	BJ	skin:	n/a
23	chr3:48957246-48957296	HRCEpiC	kidney:	n/a
24	chr3:48957246-48957296	PFSK-1	brain:	n/a
25	chr3:48957246-48957296	Caco-2	colon:	n/a
26	chr3:48957246-48957296	NT2-D1	testis:	n/a
27	chr3:48957246-48957296	HAEpiC	amniotic membrane:	n/a
28	chr3:48957246-48957296	K562	blood:	n/a
29	chr3:48957246-48957296	MCF10A-Er-Src	breast:	n/a
30	chr3:48957246-48957296	PANC-1	pancreas:	n/a
31	chr3:48957246-48957296	NHDF-neo	bronchial:	n/a
32	chr3:48957246-48957296	AG09309	skin:	n/a
33	chr3:48957246-48957296	SKMC	muscle:	n/a
34	chr3:48957246-48957296	GM12891	blood:	n/a
35	chr3:48957246-48957296	GM19239	blood:	n/a
36	chr3:48957246-48957296	HCPEpiC	choroid plexus:	n/a
37	chr3:48957246-48957296	AG09319	gingival:	n/a
38	chr3:48957246-48957296	A549	lung:	n/a
39	chr3:48957246-48957296	NHBE	bronchial:	n/a
40	chr3:48957246-48957296	SK-N-SH_RA	brain:	n/a
41	chr3:48957246-48957296	AG04449	skin:	fetal
42	chr3:48957246-48957296	Hela-S3	cervix:	n/a
43	chr3:48957246-48957296	GM12878	blood:	n/a
44	chr3:48957246-48957296	Hepatocyte	liver:	n/a
45	chr3:48957246-48957296	CMK	blood:	n/a
46	chr3:48957246-48957296	SAEC	small airway:	n/a
47	chr3:48957246-48957296	GM06990	blood:	n/a
48	chr3:48957246-48957296	U87	brain:	n/a
49	chr3:48957246-48957296	NB4	blood:	n/a
50	chr3:48957246-48957296	ProgFib	skin:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48955974..48957797-chr3:49448912..49450941,2	K562	blood:
2	chr3:48956178..48958930-chr3:48964681..48967359,2	MCF-7	breast:
3	chr3:48722838..48724823-chr3:48955919..48958463,2	K562	blood:
4	chr3:48753119..48755656-chr3:48955067..48957607,2	MCF-7	breast:
5	chr3:48955220..48957658-chr3:48960315..48963071,3	MCF-7	breast:
6	chr3:48954426..48959569-chr3:49057203..49060067,5	K562	blood:
7	chr3:48700103..48702620-chr3:48955233..48957367,3	K562	blood:
8	chr3:48700863..48702620-chr3:48955867..48958209,2	K562	blood:
9	chr3:48954616..48957728-chr3:49043769..49045935,3	K562	blood:
10	chr3:48956190..48958160-chr3:48963848..48966266,2	MCF-7	breast:
11	chr3:48777544..48781186-chr3:48954650..48958375,5	K562	blood:
12	chr3:48955694..48958185-chr3:49021057..49023573,2	K562	blood:
13	chr3:48831351..48833653-chr3:48957027..48958695,2	MCF-7	breast:
14	chr3:48882526..48886164-chr3:48952991..48958735,8	K562	blood:
15	chr3:48882526..48887589-chr3:48952932..48958567,11	K562	blood:
16	chr3:48956092..48958804-chr3:49057398..49059224,2	K562	blood:
17	chr3:48933374..48937590-chr3:48954193..48958596,7	K562	blood:

No data

Variant related genes	Relation type
ARIH2OS	TF binding region
ARIH2	TF binding region
ARIH2	CpG island
ARIH2OS	CpG island
ENSG00000228350	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000224424	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000178537	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000235236	Chromatin interaction
ENSG00000273211	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000114302	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv3394753	chr3:48956248-48960046	Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3340246	chr3:48956448-48960646	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	esv3461083	chr3:48956973-48960121	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
7	esv3346770	chr3:48957098-48959796	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
8	esv3461085	chr3:48957264-48959239	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	esv2473053	chr3:48957279-48959505	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 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	chr3:48954800-48957800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:48955000-48957600	Active TSS	Fetal Brain Female	brain
3	chr3:48955000-48957600	Active TSS	HSMM	muscle
4	chr3:48955200-48957600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:48955200-48957600	Active TSS	Fetal Intestine Small	intestine
6	chr3:48955200-48957600	Active TSS	Hela-S3	cervix
7	chr3:48955200-48957800	Active TSS	Colonic Mucosa	Colon
8	chr3:48955200-48957800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr3:48955200-48957800	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr3:48955200-48958200	Active TSS	GM12878-XiMat	blood
11	chr3:48955200-48958200	Active TSS	K562	blood
12	chr3:48955400-48957400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:48955400-48957400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr3:48955400-48957400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:48955400-48957400	Active TSS	Colon Smooth Muscle	Colon
16	chr3:48955400-48957400	Active TSS	Esophagus	oesophagus
17	chr3:48955400-48957400	Active TSS	Left Ventricle	heart
18	chr3:48955400-48957600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:48955400-48957600	Active TSS	Pancreas	Pancrea
20	chr3:48955400-48957600	Active TSS	HSMMtube	muscle
21	chr3:48955400-48957800	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:48955400-48957800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr3:48955400-48957800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:48955400-48957800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:48955400-48957800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:48955400-48957800	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr3:48955400-48957800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:48955400-48957800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:48955400-48957800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:48955400-48957800	Active TSS	Psoas Muscle	Psoas
31	chr3:48955400-48957800	Active TSS	Right Atrium	heart
32	chr3:48955400-48957800	Active TSS	Right Ventricle	heart
33	chr3:48955400-48957800	Active TSS	NHDF-Ad	bronchial
34	chr3:48955400-48957800	Active TSS	NHLF	lung
35	chr3:48955400-48958000	Active TSS	A549	lung
36	chr3:48955600-48957400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:48955600-48957400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:48955600-48957400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:48955600-48957400	Active TSS	Fetal Intestine Large	intestine
40	chr3:48955600-48957400	Active TSS	Fetal Muscle Trunk	muscle
41	chr3:48955600-48957400	Active TSS	Ovary	ovary
42	chr3:48955600-48957400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:48955600-48957400	Active TSS	Spleen	Spleen
44	chr3:48955600-48957600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr3:48955600-48957600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:48955600-48957600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:48955600-48957600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:48955600-48957600	Active TSS	Gastric	stomach
49	chr3:48955600-48957600	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr3:48955600-48957600	Active TSS	Stomach Mucosa	stomach

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