Variant report

Variant	rs556026576
Chromosome Location	chr3:49506949-49506950
allele	A/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	POLR2A	chr3:49506818-49508493	HUVEC	blood vessel:	n/a	n/a
3	RUNX3	chr3:49506880-49508289	GM12878	blood:	n/a	n/a
4	MAX	chr3:49506483-49508246	SK-N-SH	brain:	n/a	chr3:49507013-49507023
5	MAX	chr3:49506406-49508265	A549	lung:	n/a	chr3:49507013-49507023
6	NFIC	chr3:49506364-49507381	ECC-1	luminal epithelium:	n/a	chr3:49506681-49506697 chr3:49506680-49506697
7	STAT3	chr3:49506925-49507633	MCF10A-Er-Src	breast:	n/a	chr3:49507107-49507119 chr3:49507475-49507487
8	POLR2A	chr3:49506789-49508427	HepG2	liver:	n/a	n/a
9	ZBTB7A	chr3:49506706-49507079	K562	blood:	n/a	n/a
10	TBP	chr3:49506853-49508278	K562	blood:	n/a	n/a
11	POLR2A	chr3:49506874-49508282	HUVEC	blood vessel:	n/a	n/a
12	TEAD4	chr3:49506373-49507494	HepG2	liver:	n/a	n/a
13	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
14	POLR2A	chr3:49506564-49508420	K562	blood:	n/a	n/a
15	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
16	MEF2A	chr3:49506736-49507153	K562	blood:	n/a	chr3:49506970-49506984 chr3:49506969-49506984
17	RCOR1	chr3:49506855-49508336	K562	blood:	n/a	n/a
18	TCF7L2	chr3:49506929-49507426	Hela-S3	cervix:	n/a	n/a
19	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
20	POLR2A	chr3:49506849-49508242	HCT-116	colon:	n/a	n/a
21	SIN3AK20	chr3:49506466-49507175	H1-hESC	embryonic stem cell:	n/a	n/a
22	STAT3	chr3:49506916-49507454	MCF10A-Er-Src	breast:	n/a	chr3:49507107-49507119
23	POLR2A	chr3:49506948-49508349	HUVEC	blood vessel:	n/a	n/a
24	JUND	chr3:49506874-49508325	K562	blood:	n/a	chr3:49507492-49507501 chr3:49507236-49507245
25	MAX	chr3:49506940-49508329	H1-hESC	embryonic stem cell:	n/a	chr3:49507013-49507023
26	MTA3	chr3:49506876-49507494	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:49506893-49508343	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:49506940-49508356	MCF10A-Er-Src	breast:	n/a	n/a
29	TEAD4	chr3:49506388-49507335	SK-N-SH	brain:	n/a	n/a
30	TEAD4	chr3:49506429-49507427	H1-hESC	embryonic stem cell:	n/a	n/a
31	BRCA1	chr3:49506884-49507757	Hela-S3	cervix:	n/a	n/a
32	GTF2B	chr3:49506905-49507191	K562	blood:	n/a	n/a
33	GATA3	chr3:49506857-49507216	T-47D	breast:	n/a	chr3:49506902-49506913
34	NR2F2	chr3:49506944-49507561	K562	blood:	n/a	n/a
35	STAT5A	chr3:49506855-49507127	GM12878	blood:	n/a	chr3:49507107-49507119
36	SIN3A	chr3:49506507-49508607	H1-hESC	embryonic stem cell:	n/a	chr3:49507507-49507520 chr3:49506954-49506963 chr3:49507546-49507557
37	POLR2A	chr3:49506441-49508367	GM12878	blood:	n/a	n/a
38	REST	chr3:49506767-49507472	A549	lung:	n/a	n/a
39	SMC3	chr3:49506446-49508398	Hela-S3	cervix:	n/a	chr3:49506615-49506622
40	REST	chr3:49506805-49507122	SK-N-SH	brain:	n/a	n/a
41	TAF1	chr3:49506898-49508456	ECC-1	luminal epithelium:	n/a	n/a
42	RAD21	chr3:49506605-49507204	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr3:49506900-49507050	HCPEpiC	choroid plexus:	n/a	n/a
44	YY1	chr3:49506856-49507150	HCT-116	colon:	n/a	n/a
45	POLR2A	chr3:49506859-49508320	GM19193	blood:	n/a	n/a
46	MAFK	chr3:49506696-49507975	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr3:49506503-49508428	GM12892	blood:	n/a	n/a
48	POLR2A	chr3:49506510-49508430	HepG2	liver:	n/a	n/a
49	ELK1	chr3:49506942-49508066	Hela-S3	cervix:	n/a	n/a
50	NRF1	chr3:49506377-49508357	SK-N-SH	brain:	n/a	chr3:49507530-49507541

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

Variant related genes	Relation type
RNA5SP130	TF binding region
DAG1	TF binding region
ENSG00000272434	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000173402	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49503600-49507200	Weak transcription	Spleen	Spleen
2	chr3:49504000-49507000	Weak transcription	Small Intestine	intestine
3	chr3:49505600-49507000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:49505600-49507000	Enhancers	Left Ventricle	heart
5	chr3:49505800-49507000	Enhancers	Stomach Mucosa	stomach
6	chr3:49506000-49507200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:49506000-49507400	Flanking Active TSS	Hela-S3	cervix
8	chr3:49506200-49507400	Flanking Active TSS	Placenta	Placenta
9	chr3:49506200-49507400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr3:49506400-49507000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:49506400-49507000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49506400-49507000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:49506400-49507000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:49506400-49507000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:49506400-49507000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:49506400-49507000	Enhancers	Fetal Intestine Large	intestine
17	chr3:49506400-49507000	Enhancers	Fetal Thymus	thymus
18	chr3:49506400-49507000	Enhancers	Lung	lung
19	chr3:49506400-49507000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr3:49506400-49507000	Flanking Active TSS	HepG2	liver
21	chr3:49506400-49507000	Enhancers	HUVEC	blood vessel
22	chr3:49506400-49507200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49506400-49507200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:49506400-49507200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:49506400-49507200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:49506400-49507200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:49506400-49507200	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr3:49506400-49507400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:49506400-49507400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:49506400-49507400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:49506400-49507400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:49506400-49507400	Flanking Active TSS	Colonic Mucosa	Colon
33	chr3:49506400-49507400	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr3:49506400-49507400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:49506400-49507400	Flanking Active TSS	HSMMtube	muscle
36	chr3:49506400-49507600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:49506400-49507600	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr3:49506400-49507800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:49506400-49509200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr3:49506400-49509600	Active TSS	H9 Cell Line	embryonic stem cell
41	chr3:49506600-49507000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:49506600-49507000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:49506600-49507000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:49506600-49507000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:49506600-49507000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:49506600-49507000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:49506600-49507000	Enhancers	Fetal Kidney	kidney
48	chr3:49506600-49507000	Enhancers	Ovary	ovary
49	chr3:49506600-49507000	Flanking Active TSS	Right Ventricle	heart
50	chr3:49506600-49507000	Flanking Active TSS	A549	lung

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