Variant report

Variant	rs542395993
Chromosome Location	chr3:49507409-49507410
allele	C/G
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	NFYA	chr3:49507407-49507712	K562	blood:	n/a	chr3:49507488-49507502 chr3:49507488-49507503 chr3:49507488-49507501 chr3:49507490-49507500 chr3:49507490-49507500 chr3:49507488-49507503
3	POLR2A	chr3:49507204-49508280	NB4	blood:	n/a	n/a
4	POLR2A	chr3:49506818-49508493	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:49507218-49507528	K562	blood:	n/a	n/a
6	RUNX3	chr3:49506880-49508289	GM12878	blood:	n/a	n/a
7	YY1	chr3:49507234-49508155	GM12891	blood:	n/a	chr3:49508131-49508145 chr3:49507664-49507678 chr3:49507592-49507606 chr3:49507665-49507679
8	YY1	chr3:49507140-49508274	GM12878	blood:	n/a	chr3:49508131-49508145 chr3:49507664-49507678 chr3:49507592-49507606 chr3:49507665-49507679
9	MAX	chr3:49506483-49508246	SK-N-SH	brain:	n/a	chr3:49507013-49507023
10	MXI1	chr3:49507075-49508289	HepG2	liver:	n/a	n/a
11	MAX	chr3:49506406-49508265	A549	lung:	n/a	chr3:49507013-49507023
12	STAT3	chr3:49506925-49507633	MCF10A-Er-Src	breast:	n/a	chr3:49507107-49507119 chr3:49507475-49507487
13	POLR2A	chr3:49507166-49508289	GM10847	blood:	n/a	n/a
14	POLR2A	chr3:49506789-49508427	HepG2	liver:	n/a	n/a
15	TAF1	chr3:49507236-49507459	GM12892	blood:	n/a	n/a
16	TEAD4	chr3:49507175-49507519	K562	blood:	n/a	n/a
17	SP4	chr3:49507032-49507558	H1-hESC	embryonic stem cell:	n/a	chr3:49507513-49507529 chr3:49507476-49507492
18	PML	chr3:49507113-49507473	K562	blood:	n/a	n/a
19	BHLHE40	chr3:49507202-49507815	HepG2	liver:	n/a	chr3:49507598-49507614
20	TBP	chr3:49506853-49508278	K562	blood:	n/a	n/a
21	POLR2A	chr3:49506874-49508282	HUVEC	blood vessel:	n/a	n/a
22	MAX	chr3:49507092-49508305	NB4	blood:	n/a	n/a
23	TEAD4	chr3:49506373-49507494	HepG2	liver:	n/a	n/a
24	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
25	POLR2A	chr3:49507160-49508256	HepG2	liver:	n/a	n/a
26	POLR2A	chr3:49506564-49508420	K562	blood:	n/a	n/a
27	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
28	MYC	chr3:49507003-49508275	K562	blood:	n/a	chr3:49507013-49507023
29	RCOR1	chr3:49506855-49508336	K562	blood:	n/a	n/a
30	TAF1	chr3:49506972-49507531	PFSK-1	brain:	n/a	n/a
31	TBL1XR1	chr3:49507284-49507435	K562	blood:	n/a	n/a
32	POLR2A	chr3:49507154-49508220	HepG2	liver:	n/a	n/a
33	TCF7L2	chr3:49506929-49507426	Hela-S3	cervix:	n/a	n/a
34	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
35	POLR2A	chr3:49506849-49508242	HCT-116	colon:	n/a	n/a
36	STAT3	chr3:49506916-49507454	MCF10A-Er-Src	breast:	n/a	chr3:49507107-49507119
37	POLR2A	chr3:49506955-49508272	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:49506948-49508349	HUVEC	blood vessel:	n/a	n/a
39	JUND	chr3:49506874-49508325	K562	blood:	n/a	chr3:49507492-49507501 chr3:49507236-49507245
40	MAX	chr3:49506940-49508329	H1-hESC	embryonic stem cell:	n/a	chr3:49507013-49507023
41	MTA3	chr3:49506876-49507494	GM12878	blood:	n/a	n/a
42	TAF1	chr3:49507159-49507433	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:49506893-49508343	GM12878	blood:	n/a	n/a
44	TAF1	chr3:49507242-49507536	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr3:49506940-49508356	MCF10A-Er-Src	breast:	n/a	n/a
46	YY1	chr3:49507104-49507547	GM12878	blood:	n/a	n/a
47	TEAD4	chr3:49506429-49507427	H1-hESC	embryonic stem cell:	n/a	n/a
48	BRCA1	chr3:49506884-49507757	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr3:49506987-49507501	GM12892	blood:	n/a	n/a
50	TAF1	chr3:49507270-49507596	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49507385-49507435	SKMC	muscle:	n/a
2	chr3:49507385-49507435	HCF	heart:	n/a
3	chr3:49507385-49507435	BE2_C	brain:	n/a
4	chr3:49507385-49507435	HEK293	kidney:	embryo
5	chr3:49507385-49507435	HNPCEpiC	eye:	n/a
6	chr3:49507385-49507435	AoSMC	blood vessel:	n/a
7	chr3:49507385-49507435	AG09309	skin:	n/a
8	chr3:49507385-49507435	K562	blood:	n/a
9	chr3:49507385-49507435	HIPEpiC	eye:	n/a
10	chr3:49507385-49507435	GM19239	blood:	n/a
11	chr3:49507385-49507435	H1-hESC	embryonic stem cell:	embryo
12	chr3:49507385-49507435	BJ	skin:	n/a
13	chr3:49507385-49507435	HRPEpiC	eye:	n/a
14	chr3:49507385-49507435	NB4	blood:	n/a
15	chr3:49507385-49507435	PANC-1	pancreas:	n/a
16	chr3:49507385-49507435	RPTEC	kidney:	n/a
17	chr3:49507385-49507435	Jurkat	blood:	n/a
18	chr3:49507385-49507435	U87	brain:	n/a
19	chr3:49507385-49507435	CMK	blood:	n/a
20	chr3:49507385-49507435	HMEC	breast:	n/a
21	chr3:49507385-49507435	A549	lung:	n/a
22	chr3:49507385-49507435	ECC-1	luminal epithelium:	n/a
23	chr3:49507385-49507435	MCF-7	breast:	n/a
24	chr3:49507385-49507435	GM12892	blood:	n/a
25	chr3:49507385-49507435	SK-N-SH	brain:	n/a
26	chr3:49507385-49507435	HL-60	blood:	n/a
27	chr3:49507385-49507435	Hela-S3	cervix:	n/a
28	chr3:49507385-49507435	HCM	heart:	n/a
29	chr3:49507385-49507435	PrEC	prostate:	n/a
30	chr3:49507385-49507435	HCT-116	colon:	n/a
31	chr3:49507385-49507435	LNCaP	prostate:	n/a
32	chr3:49507385-49507435	HAEpiC	amniotic membrane:	n/a
33	chr3:49507385-49507435	T-47D	breast:	n/a
34	chr3:49507385-49507435	NHDF-neo	bronchial:	n/a
35	chr3:49507385-49507435	SAEC	small airway:	n/a
36	chr3:49507385-49507435	HRE	kidney:	n/a
37	chr3:49507385-49507435	HUVEC	blood vessel:	n/a
38	chr3:49507385-49507435	Hepatocyte	liver:	n/a
39	chr3:49507385-49507435	AG04450	lung:	fetal
40	chr3:49507385-49507435	SK-N-MC	brain:	n/a
41	chr3:49507385-49507435	NT2-D1	testis:	n/a
42	chr3:49507385-49507435	AG09319	gingival:	n/a
43	chr3:49507385-49507435	NHBE	bronchial:	n/a
44	chr3:49507385-49507435	GM06990	blood:	n/a
45	chr3:49507385-49507435	PFSK-1	brain:	n/a
46	chr3:49507385-49507435	ovcar-3	ovarian:	n/a
47	chr3:49507385-49507435	AG04449	skin:	fetal
48	chr3:49507385-49507435	IMR90	lung:	fetal
49	chr3:49507385-49507435	HepG2	liver:	n/a
50	chr3:49507385-49507435	Caco-2	colon:	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	chr3:49503012..49504721-chr3:49506646..49509185,2	MCF-7	breast:
15	chr3:49506879..49507449-chr7:45018883..45019516,2	Hela-S3	cervix:
16	chr3:49376524..49378988-chr3:49507303..49509521,2	MCF-7	breast:
17	chr3:49065352..49067075-chr3:49506284..49508355,2	K562	blood:

Variant related genes	Relation type
RNA5SP130	TF binding region
DAG1	TF binding region
DAG1	CpG island
RNA5SP130	CpG island
ENSG00000207605	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000253744	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000153914	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000272434	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	chr3:49506400-49507600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:49506400-49507600	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr3:49506400-49507800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:49506400-49509200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:49506400-49509600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:49506800-49507600	Weak transcription	Gastric	stomach
7	chr3:49506800-49507600	Active TSS	Right Atrium	heart
8	chr3:49506800-49508400	Active TSS	Brain Angular Gyrus	brain
9	chr3:49506800-49508600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:49506800-49508800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:49506800-49509200	Active TSS	Psoas Muscle	Psoas
12	chr3:49507000-49508600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:49507000-49508600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:49507000-49508600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:49507000-49508600	Active TSS	Fetal Kidney	kidney
16	chr3:49507000-49508800	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:49507000-49508800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:49507000-49508800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:49507000-49508800	Active TSS	Lung	lung
20	chr3:49507000-49508800	Active TSS	Ovary	ovary
21	chr3:49507000-49509000	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:49507000-49509000	Active TSS	Aorta	Aorta
23	chr3:49507000-49509000	Active TSS	A549	lung
24	chr3:49507200-49508200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:49507200-49508200	Active TSS	Brain Anterior Caudate	brain
26	chr3:49507200-49508200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:49507200-49508400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:49507200-49508400	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr3:49507200-49508400	Active TSS	Brain Cingulate Gyrus	brain
30	chr3:49507200-49508400	Active TSS	Brain Germinal Matrix	brain
31	chr3:49507200-49508400	Active TSS	Brain Hippocampus Middle	brain
32	chr3:49507200-49508400	Active TSS	Fetal Lung	lung
33	chr3:49507200-49508400	Active TSS	Placenta Amnion	Placenta Amnion
34	chr3:49507200-49508400	Active TSS	Spleen	Spleen
35	chr3:49507200-49508600	Active TSS	H1 Cell Line	embryonic stem cell
36	chr3:49507200-49508600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:49507200-49508600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:49507200-49508600	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:49507200-49508600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:49507200-49508600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:49507200-49508600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr3:49507200-49508600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:49507200-49508600	Active TSS	Brain Substantia Nigra	brain
44	chr3:49507200-49508600	Active TSS	Colon Smooth Muscle	Colon
45	chr3:49507200-49508600	Active TSS	Duodenum Mucosa	Duodenum
46	chr3:49507200-49508600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:49507200-49508600	Active TSS	Fetal Brain Female	brain
48	chr3:49507200-49508600	Active TSS	Fetal Intestine Large	intestine
49	chr3:49507200-49508600	Active TSS	Fetal Stomach	stomach
50	chr3:49507200-49508600	Active TSS	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links