Variant report

Variant	rs139896371
Chromosome Location	chr3:49507204-49507205
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:49506252-49509681	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:49507204-49508280	NB4	blood:	n/a	n/a
3	POLR2A	chr3:49506818-49508493	HUVEC	blood vessel:	n/a	n/a
4	RUNX3	chr3:49506880-49508289	GM12878	blood:	n/a	n/a
5	YY1	chr3:49507140-49508274	GM12878	blood:	n/a	chr3:49508131-49508145 chr3:49507664-49507678 chr3:49507592-49507606 chr3:49507665-49507679
6	MAX	chr3:49506483-49508246	SK-N-SH	brain:	n/a	chr3:49507013-49507023
7	MXI1	chr3:49507075-49508289	HepG2	liver:	n/a	n/a
8	MAX	chr3:49506406-49508265	A549	lung:	n/a	chr3:49507013-49507023
9	NFIC	chr3:49506364-49507381	ECC-1	luminal epithelium:	n/a	chr3:49506681-49506697 chr3:49506680-49506697
10	STAT3	chr3:49506925-49507633	MCF10A-Er-Src	breast:	n/a	chr3:49507107-49507119 chr3:49507475-49507487
11	POLR2A	chr3:49507166-49508289	GM10847	blood:	n/a	n/a
12	POLR2A	chr3:49506789-49508427	HepG2	liver:	n/a	n/a
13	TEAD4	chr3:49507175-49507519	K562	blood:	n/a	n/a
14	SP4	chr3:49507032-49507558	H1-hESC	embryonic stem cell:	n/a	chr3:49507513-49507529 chr3:49507476-49507492
15	PML	chr3:49507113-49507473	K562	blood:	n/a	n/a
16	BHLHE40	chr3:49507202-49507815	HepG2	liver:	n/a	chr3:49507598-49507614
17	TBP	chr3:49506853-49508278	K562	blood:	n/a	n/a
18	POLR2A	chr3:49506874-49508282	HUVEC	blood vessel:	n/a	n/a
19	MAX	chr3:49507092-49508305	NB4	blood:	n/a	n/a
20	TEAD4	chr3:49506373-49507494	HepG2	liver:	n/a	n/a
21	SP1	chr3:49506683-49507734	A549	lung:	n/a	chr3:49507515-49507527 chr3:49507353-49507362 chr3:49507015-49507029 chr3:49507515-49507527 chr3:49507351-49507363 chr3:49507672-49507681 chr3:49507019-49507028 chr3:49507516-49507525 chr3:49507479-49507489 chr3:49507517-49507526 chr3:49507352-49507366 chr3:49507479-49507489 chr3:49507352-49507361 chr3:49507671-49507683 chr3:49507671-49507683 chr3:49507352-49507362 chr3:49507018-49507030 chr3:49507489-49507510 chr3:49507351-49507363 chr3:49507517-49507526
22	POLR2A	chr3:49507160-49508256	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:49506564-49508420	K562	blood:	n/a	n/a
24	SP1	chr3:49506796-49507777	A549	lung:	n/a	chr3:49507515-49507527 chr3:49507353-49507362 chr3:49507015-49507029 chr3:49507515-49507527 chr3:49507351-49507363 chr3:49507672-49507681 chr3:49507019-49507028 chr3:49507516-49507525 chr3:49507479-49507489 chr3:49507517-49507526 chr3:49507352-49507366 chr3:49507479-49507489 chr3:49507352-49507361 chr3:49507671-49507683 chr3:49507671-49507683 chr3:49507352-49507362 chr3:49507018-49507030 chr3:49507489-49507510 chr3:49507351-49507363 chr3:49507517-49507526
25	MYC	chr3:49507003-49508275	K562	blood:	n/a	chr3:49507013-49507023
26	RCOR1	chr3:49506855-49508336	K562	blood:	n/a	n/a
27	TAF1	chr3:49506972-49507531	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr3:49507154-49508220	HepG2	liver:	n/a	n/a
29	TCF7L2	chr3:49506929-49507426	Hela-S3	cervix:	n/a	n/a
30	RFX5	chr3:49506541-49508416	Hela-S3	cervix:	n/a	chr3:49507491-49507500 chr3:49507276-49507285 chr3:49507650-49507664 chr3:49507647-49507662 chr3:49507651-49507660 chr3:49507649-49507665 chr3:49507648-49507662
31	POLR2A	chr3:49506849-49508242	HCT-116	colon:	n/a	n/a
32	STAT3	chr3:49506916-49507454	MCF10A-Er-Src	breast:	n/a	chr3:49507107-49507119
33	POLR2A	chr3:49506955-49508272	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:49506948-49508349	HUVEC	blood vessel:	n/a	n/a
35	JUND	chr3:49506874-49508325	K562	blood:	n/a	chr3:49507492-49507501 chr3:49507236-49507245
36	MAX	chr3:49506940-49508329	H1-hESC	embryonic stem cell:	n/a	chr3:49507013-49507023
37	MTA3	chr3:49506876-49507494	GM12878	blood:	n/a	n/a
38	TAF1	chr3:49507159-49507433	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:49506893-49508343	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:49506940-49508356	MCF10A-Er-Src	breast:	n/a	n/a
41	TEAD4	chr3:49506388-49507335	SK-N-SH	brain:	n/a	n/a
42	YY1	chr3:49507104-49507547	GM12878	blood:	n/a	n/a
43	TEAD4	chr3:49506429-49507427	H1-hESC	embryonic stem cell:	n/a	n/a
44	BRCA1	chr3:49506884-49507757	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr3:49506987-49507501	GM12892	blood:	n/a	n/a
46	EBF1	chr3:49507172-49508077	GM12878	blood:	n/a	n/a
47	RFX5	chr3:49507177-49508018	HepG2	liver:	n/a	chr3:49507491-49507500 chr3:49507276-49507285 chr3:49507650-49507664 chr3:49507647-49507662 chr3:49507651-49507660 chr3:49507649-49507665 chr3:49507648-49507662
48	GATA3	chr3:49506857-49507216	T-47D	breast:	n/a	chr3:49506902-49506913
49	POLR2A	chr3:49507199-49508287	HEK293	kidney:	n/a	n/a
50	POLR2A	chr3:49507202-49508179	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49507186-49507236	PANC-1	pancreas:	n/a
2	chr3:49507186-49507236	GM19239	blood:	n/a
3	chr3:49507186-49507236	T-47D	breast:	n/a
4	chr3:49507186-49507236	Hela-S3	cervix:	n/a
5	chr3:49507186-49507236	BE2_C	brain:	n/a
6	chr3:49507186-49507236	ovcar-3	ovarian:	n/a
7	chr3:49507186-49507236	NHBE	bronchial:	n/a
8	chr3:49507186-49507236	GM12878	blood:	n/a
9	chr3:49507186-49507236	K562	blood:	n/a
10	chr3:49507186-49507236	H1-hESC	embryonic stem cell:	embryo
11	chr3:49507186-49507236	SK-N-SH	brain:	n/a
12	chr3:49507186-49507236	ProgFib	skin:	n/a
13	chr3:49507186-49507236	HCF	heart:	n/a
14	chr3:49507186-49507236	HEEpiC	esophagus:	n/a
15	chr3:49507186-49507236	HL-60	blood:	n/a
16	chr3:49507186-49507236	HRPEpiC	eye:	n/a
17	chr3:49507186-49507236	Jurkat	blood:	n/a
18	chr3:49507186-49507236	AoSMC	blood vessel:	n/a
19	chr3:49507186-49507236	MCF10A-Er-Src	breast:	n/a
20	chr3:49507186-49507236	MCF-7	breast:	n/a
21	chr3:49507186-49507236	AG04449	skin:	fetal
22	chr3:49507186-49507236	NH-A	brain:	n/a
23	chr3:49507186-49507236	ECC-1	luminal epithelium:	n/a
24	chr3:49507186-49507236	HNPCEpiC	eye:	n/a
25	chr3:49507186-49507236	BJ	skin:	n/a
26	chr3:49507186-49507236	PrEC	prostate:	n/a
27	chr3:49507186-49507236	Caco-2	colon:	n/a
28	chr3:49507186-49507236	SKMC	muscle:	n/a
29	chr3:49507186-49507236	HAEpiC	amniotic membrane:	n/a
30	chr3:49507186-49507236	RPTEC	kidney:	n/a
31	chr3:49507186-49507236	IMR90	lung:	fetal
32	chr3:49507186-49507236	U87	brain:	n/a
33	chr3:49507186-49507236	SK-N-SH_RA	brain:	n/a
34	chr3:49507186-49507236	NHDF-neo	bronchial:	n/a
35	chr3:49507186-49507236	HCT-116	colon:	n/a
36	chr3:49507186-49507236	HCM	heart:	n/a
37	chr3:49507186-49507236	HEK293	kidney:	embryo
38	chr3:49507186-49507236	HMEC	breast:	n/a
39	chr3:49507186-49507236	GM12891	blood:	n/a
40	chr3:49507186-49507236	PFSK-1	brain:	n/a
41	chr3:49507186-49507236	Hepatocyte	liver:	n/a
42	chr3:49507186-49507236	SAEC	small airway:	n/a
43	chr3:49507186-49507236	AG09309	skin:	n/a
44	chr3:49507186-49507236	AG04450	lung:	fetal
45	chr3:49507186-49507236	LNCaP	prostate:	n/a
46	chr3:49507186-49507236	HUVEC	blood vessel:	n/a
47	chr3:49507186-49507236	HepG2	liver:	n/a
48	chr3:49507186-49507236	SK-N-MC	brain:	n/a
49	chr3:49507186-49507236	AG09319	gingival:	n/a
50	chr3:49507186-49507236	GM12892	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
2	chr3:49507200..49507717-chr5:65440276..65440998,2	Hela-S3	cervix:
3	chr3:49506988..49509379-chr3:49529279..49532110,2	MCF-7	breast:
4	chr3:49506481..49509131-chr3:49546764..49549304,2	MCF-7	breast:
5	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
6	chr3:49506444..49509653-chr3:49710909..49714606,3	K562	blood:
7	chr3:49056423..49060378-chr3:49506507..49510634,4	K562	blood:
8	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
9	chr3:49505441..49508480-chr3:49710122..49713377,5	MCF-7	breast:
10	chr16:30536975..30539864-chr3:49506980..49509217,2	MCF-7	breast:
11	chr3:49501861..49505109-chr3:49505439..49508808,5	K562	blood:
12	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
13	chr3:49460325..49461920-chr3:49506460..49509220,2	MCF-7	breast:
14	chr3:49043383..49045852-chr3:49505855..49507402,2	MCF-7	breast:
15	chr3:49503012..49504721-chr3:49506646..49509185,2	MCF-7	breast:
16	chr3:49506879..49507449-chr7:45018883..45019516,2	Hela-S3	cervix:
17	chr3:49065352..49067075-chr3:49506284..49508355,2	K562	blood:

Variant related genes	Relation type
RNA5SP130	TF binding region
DAG1	TF binding region
RNA5SP130	CpG island
DAG1	CpG island
ENSG00000272434	Chromatin interaction
ENSG00000153914	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000253744	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000178035	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3420339	chr3:49505548-49510046	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv3439400	chr3:49506373-49508921	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3380038	chr3:49506748-49508796	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	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	chr3:49506000-49507400	Flanking Active TSS	Hela-S3	cervix
2	chr3:49506200-49507400	Flanking Active TSS	Placenta	Placenta
3	chr3:49506200-49507400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr3:49506400-49507400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:49506400-49507400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:49506400-49507400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:49506400-49507400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:49506400-49507400	Flanking Active TSS	Colonic Mucosa	Colon
9	chr3:49506400-49507400	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr3:49506400-49507400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr3:49506400-49507400	Flanking Active TSS	HSMMtube	muscle
12	chr3:49506400-49507600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:49506400-49507600	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr3:49506400-49507800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:49506400-49509200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:49506400-49509600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:49506600-49507400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:49506600-49507400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:49506600-49507400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:49506600-49507400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:49506600-49507400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr3:49506600-49507400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:49506600-49507400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:49506600-49507400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:49506600-49507400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:49506600-49507400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:49506600-49507400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr3:49506600-49507400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr3:49506600-49507400	Flanking Active TSS	Fetal Muscle Trunk	muscle
30	chr3:49506600-49507400	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr3:49506600-49507400	Flanking Active TSS	Pancreas	Pancrea
32	chr3:49506600-49507400	Flanking Active TSS	HMEC	breast
33	chr3:49506600-49507400	Flanking Active TSS	HSMM	muscle
34	chr3:49506600-49507400	Flanking Active TSS	K562	blood
35	chr3:49506600-49507400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:49506600-49507400	Flanking Active TSS	NH-A	brain
37	chr3:49506600-49507400	Flanking Active TSS	NHDF-Ad	bronchial
38	chr3:49506600-49507400	Flanking Active TSS	NHEK	skin
39	chr3:49506600-49507400	Flanking Active TSS	NHLF	lung
40	chr3:49506600-49507400	Flanking Active TSS	Osteobl	bone
41	chr3:49506800-49507400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr3:49506800-49507400	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr3:49506800-49507400	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr3:49506800-49507400	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr3:49506800-49507400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr3:49506800-49507400	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr3:49506800-49507400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:49506800-49507400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr3:49506800-49507400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr3:49506800-49507400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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