Variant report

Variant	rs28364662
Chromosome Location	chr3:49508251-49508252
allele	C/T
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	POU2F2	chr3:49507929-49508253	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:49506880-49508289	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:49507641-49508255	GM12891	blood:	n/a	n/a
7	ZMIZ1	chr3:49507791-49508258	K562	blood:	n/a	n/a
8	YY1	chr3:49507140-49508274	GM12878	blood:	n/a	chr3:49508131-49508145 chr3:49507664-49507678 chr3:49507592-49507606 chr3:49507665-49507679
9	MXI1	chr3:49507075-49508289	HepG2	liver:	n/a	n/a
10	MAX	chr3:49506406-49508265	A549	lung:	n/a	chr3:49507013-49507023
11	POLR2A	chr3:49507166-49508289	GM10847	blood:	n/a	n/a
12	POLR2A	chr3:49506789-49508427	HepG2	liver:	n/a	n/a
13	RAD21	chr3:49508145-49508428	Hela-S3	cervix:	n/a	n/a
14	TBP	chr3:49506853-49508278	K562	blood:	n/a	n/a
15	POLR2A	chr3:49506874-49508282	HUVEC	blood vessel:	n/a	n/a
16	MAX	chr3:49507092-49508305	NB4	blood:	n/a	n/a
17	YY1	chr3:49507858-49508338	K562	blood:	n/a	chr3:49508131-49508145 chr3:49508280-49508291
18	POLR2A	chr3:49507160-49508256	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:49506564-49508420	K562	blood:	n/a	n/a
20	FOXM1	chr3:49507614-49508355	GM12878	blood:	n/a	n/a
21	MYC	chr3:49507003-49508275	K562	blood:	n/a	chr3:49507013-49507023
22	CTCF	chr3:49508160-49508310	GM12865	blood:	n/a	chr3:49508177-49508190
23	RCOR1	chr3:49506855-49508336	K562	blood:	n/a	n/a
24	POLR2A	chr3:49507588-49508469	HL-60	blood:	n/a	n/a
25	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
26	CTCF	chr3:49508120-49508270	GM12867	blood:	n/a	chr3:49508177-49508190
27	POLR2A	chr3:49506955-49508272	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:49506948-49508349	HUVEC	blood vessel:	n/a	n/a
29	JUND	chr3:49506874-49508325	K562	blood:	n/a	chr3:49507492-49507501 chr3:49507236-49507245
30	MAX	chr3:49506940-49508329	H1-hESC	embryonic stem cell:	n/a	chr3:49507013-49507023
31	CTCF	chr3:49508160-49508310	AG04450	lung:	n/a	chr3:49508177-49508190
32	CTCF	chr3:49508220-49508370	HRE	kidney:	n/a	n/a
33	POLR2A	chr3:49506893-49508343	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:49506940-49508356	MCF10A-Er-Src	breast:	n/a	n/a
35	TCF3	chr3:49507469-49508308	GM12878	blood:	n/a	chr3:49507945-49507954 chr3:49507942-49507957 chr3:49507942-49507956 chr3:49507946-49507959
36	CTCF	chr3:49508180-49508330	AoAF	blood vessel:	n/a	n/a
37	USF2	chr3:49508210-49508262	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:49507199-49508287	HEK293	kidney:	n/a	n/a
39	FOXA1	chr3:49508139-49508471	HepG2	liver:	n/a	chr3:49508357-49508372
40	CTBP2	chr3:49507721-49508261	H1-hESC	embryonic stem cell:	n/a	n/a
41	TBL1XR1	chr3:49508242-49508354	K562	blood:	n/a	n/a
42	SIN3A	chr3:49506507-49508607	H1-hESC	embryonic stem cell:	n/a	chr3:49507507-49507520 chr3:49506954-49506963 chr3:49507546-49507557
43	POLR2A	chr3:49506441-49508367	GM12878	blood:	n/a	n/a
44	CTCF	chr3:49508160-49508310	BJ	skin:	n/a	chr3:49508177-49508190
45	POLR2A	chr3:49506973-49508356	PFSK-1	brain:	n/a	n/a
46	MXI1	chr3:49507188-49508268	K562	blood:	n/a	n/a
47	SMC3	chr3:49506446-49508398	Hela-S3	cervix:	n/a	chr3:49506615-49506622
48	TAF1	chr3:49506898-49508456	ECC-1	luminal epithelium:	n/a	n/a
49	CTCF	chr3:49508160-49508310	HMEC	breast:	n/a	chr3:49508177-49508190
50	POLR2A	chr3:49506859-49508320	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
2	chr3:49507792..49509395-chr3:49538517..49540372,2	MCF-7	breast:
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	chr3:49130007..49132020-chr3:49507888..49509693,2	K562	blood:
13	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
14	chr3:49448736..49451146-chr3:49507489..49509395,2	MCF-7	breast:
15	chr3:49460325..49461920-chr3:49506460..49509220,2	MCF-7	breast:
16	chr3:49507518..49508282-chr5:43515171..43515703,2	Hela-S3	cervix:
17	chr3:49503012..49504721-chr3:49506646..49509185,2	MCF-7	breast:
18	chr3:49507807..49509484-chr3:49555798..49559257,3	MCF-7	breast:
19	chr3:49507938..49509712-chr3:49512685..49515016,2	K562	blood:
20	chr3:49376524..49378988-chr3:49507303..49509521,2	MCF-7	breast:
21	chr3:49065352..49067075-chr3:49506284..49508355,2	K562	blood:
22	chr3:49455358..49458192-chr3:49507443..49509538,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP130	TF binding region
ENSG00000235261	Chromatin interaction
ENSG00000145020	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000201301	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000178035	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49506400-49509200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49506400-49509600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:49506800-49508400	Active TSS	Brain Angular Gyrus	brain
4	chr3:49506800-49508600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:49506800-49508800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:49506800-49509200	Active TSS	Psoas Muscle	Psoas
7	chr3:49507000-49508600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:49507000-49508600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:49507000-49508600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr3:49507000-49508600	Active TSS	Fetal Kidney	kidney
11	chr3:49507000-49508800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:49507000-49508800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:49507000-49508800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:49507000-49508800	Active TSS	Lung	lung
15	chr3:49507000-49508800	Active TSS	Ovary	ovary
16	chr3:49507000-49509000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr3:49507000-49509000	Active TSS	Aorta	Aorta
18	chr3:49507000-49509000	Active TSS	A549	lung
19	chr3:49507200-49508400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:49507200-49508400	Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr3:49507200-49508400	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:49507200-49508400	Active TSS	Brain Germinal Matrix	brain
23	chr3:49507200-49508400	Active TSS	Brain Hippocampus Middle	brain
24	chr3:49507200-49508400	Active TSS	Fetal Lung	lung
25	chr3:49507200-49508400	Active TSS	Placenta Amnion	Placenta Amnion
26	chr3:49507200-49508400	Active TSS	Spleen	Spleen
27	chr3:49507200-49508600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr3:49507200-49508600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49507200-49508600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:49507200-49508600	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr3:49507200-49508600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:49507200-49508600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:49507200-49508600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr3:49507200-49508600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:49507200-49508600	Active TSS	Brain Substantia Nigra	brain
36	chr3:49507200-49508600	Active TSS	Colon Smooth Muscle	Colon
37	chr3:49507200-49508600	Active TSS	Duodenum Mucosa	Duodenum
38	chr3:49507200-49508600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:49507200-49508600	Active TSS	Fetal Brain Female	brain
40	chr3:49507200-49508600	Active TSS	Fetal Intestine Large	intestine
41	chr3:49507200-49508600	Active TSS	Fetal Stomach	stomach
42	chr3:49507200-49508600	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr3:49507200-49508600	Active TSS	GM12878-XiMat	blood
44	chr3:49507200-49508800	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr3:49507200-49508800	Active TSS	Esophagus	oesophagus
46	chr3:49507200-49508800	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:49507200-49508800	Active TSS	Small Intestine	intestine
48	chr3:49507200-49509000	Active TSS	Fetal Intestine Small	intestine
49	chr3:49507200-49509200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:49507200-49509200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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