Variant report

Variant	rs546365402
Chromosome Location	chr7:5458493-5458494
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	TEAD4	chr7:5458087-5458643	HepG2	liver:	n/a	chr7:5458425-5458434
2	CTCF	chr7:5458460-5458610	MCF-7	breast:	n/a	chr7:5458473-5458491
3	RAD21	chr7:5458085-5458728	MCF-7	breast:	n/a	chr7:5458471-5458490
4	POLR2A	chr7:5458245-5459277	HepG2	liver:	n/a	n/a
5	RAD21	chr7:5458307-5458842	IMR90	lung:	n/a	chr7:5458471-5458490
6	TEAD4	chr7:5458193-5458658	H1-hESC	embryonic stem cell:	n/a	chr7:5458425-5458434
7	EP300	chr7:5458139-5458515	K562	blood:	n/a	chr7:5458278-5458288
8	ARID3A	chr7:5458368-5458539	HepG2	liver:	n/a	n/a
9	MAZ	chr7:5457576-5459985	IMR90	lung:	n/a	chr7:5459045-5459055 chr7:5459206-5459216
10	FOSL2	chr7:5458122-5458873	MCF-7	breast:	n/a	chr7:5458823-5458834
11	BCL3	chr7:5458034-5459081	A549	lung:	n/a	n/a
12	EP300	chr7:5458066-5458931	T-47D	breast:	n/a	chr7:5458278-5458288
13	SIN3AK20	chr7:5458154-5458578	PFSK-1	brain:	n/a	n/a
14	ZKSCAN1	chr7:5458109-5459038	Hela-S3	cervix:	n/a	chr7:5458734-5458747
15	ATF2	chr7:5458219-5458881	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr7:5457870-5459053	Hela-S3	cervix:	n/a	n/a
17	HMGN3	chr7:5458174-5459075	K562	blood:	n/a	n/a
18	REST	chr7:5457985-5459093	A549	lung:	n/a	chr7:5458637-5458646 chr7:5458179-5458186
19	ZNF217	chr7:5458070-5458622	MCF-7	breast:	n/a	n/a
20	RAD21	chr7:5458269-5458689	H1-hESC	embryonic stem cell:	n/a	chr7:5458471-5458490
21	RCOR1	chr7:5458167-5458858	K562	blood:	n/a	n/a
22	POLR2A	chr7:5458134-5458978	Hela-S3	cervix:	n/a	n/a
23	MYBL2	chr7:5458071-5459120	HepG2	liver:	n/a	n/a
24	MAX	chr7:5458112-5459149	A549	lung:	n/a	chr7:5459045-5459055
25	GTF2F1	chr7:5457810-5458950	Hela-S3	cervix:	n/a	n/a
26	E2F6	chr7:5458144-5459035	H1-hESC	embryonic stem cell:	n/a	chr7:5458631-5458641
27	TAF1	chr7:5457904-5459131	H1-neurons	neurons:	n/a	n/a
28	MYC	chr7:5458196-5458586	K562	blood:	n/a	n/a
29	POLR2A	chr7:5458395-5459190	HepG2	liver:	n/a	n/a
30	MAX	chr7:5458003-5459196	HCT-116	colon:	n/a	chr7:5459045-5459055
31	EP300	chr7:5457950-5458997	A549	lung:	n/a	chr7:5458278-5458288 chr7:5458945-5458958
32	RAD21	chr7:5458341-5458602	HepG2	liver:	n/a	chr7:5458471-5458490
33	MXI1	chr7:5458312-5458847	H1-hESC	embryonic stem cell:	n/a	n/a
34	GATA3	chr7:5456781-5458965	T-47D	breast:	n/a	chr7:5457594-5457602 chr7:5457443-5457450 chr7:5457436-5457457 chr7:5457443-5457452 chr7:5458506-5458514 chr7:5457589-5457597 chr7:5457823-5457831 chr7:5457632-5457640 chr7:5457442-5457452 chr7:5457614-5457622
35	TCF7L2	chr7:5458003-5458950	HEK293	kidney:	n/a	n/a
36	POLR2A	chr7:5458473-5459083	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr7:5458103-5459178	MCF-7	breast:	n/a	n/a
38	RCOR1	chr7:5457965-5459010	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr7:5458400-5458550	AG09319	gingival:	n/a	chr7:5458473-5458491
40	TCF12	chr7:5457922-5458864	ECC-1	luminal epithelium:	n/a	n/a
41	KAP1	chr7:5458096-5458855	U2OS	brain:	n/a	n/a
42	MAFK	chr7:5458142-5458972	Hela-S3	cervix:	n/a	n/a
43	FOXA2	chr7:5458159-5458672	A549	lung:	n/a	chr7:5458283-5458295
44	BRCA1	chr7:5458335-5458505	H1-hESC	embryonic stem cell:	n/a	n/a
45	ELF1	chr7:5457992-5459351	MCF-7	breast:	n/a	n/a
46	CTCF	chr7:5458440-5458590	HA-sp	spinal cord:	n/a	chr7:5458473-5458491
47	SP1	chr7:5457879-5459050	A549	lung:	n/a	chr7:5458561-5458572 chr7:5458562-5458571
48	USF2	chr7:5458307-5458495	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr7:5458380-5458530	HPAF	blood vessel:	n/a	chr7:5458473-5458491
50	CTCF	chr7:5458380-5458530	AG04449	skin:	n/a	chr7:5458473-5458491

No.	Distal block	Cell Line	Cell type
1	chr7:5456513..5458866-chr7:5593273..5595987,2	MCF-7	breast:
2	chr7:5458325..5469295-chr7:5567159..5574053,21	MCF-7	breast:
3	chr7:5458325..5461852-chr7:5568883..5572530,6	MCF-7	breast:
4	chr7:5458255..5459132-chr7:5468021..5469070,3	MCF-7	breast:
5	chr7:5405158..5408659-chr7:5455520..5459271,4	MCF-7	breast:
6	chr7:5405741..5406385-chr7:5458033..5458970,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188365	TF binding region
ENSG00000241269	TF binding region
ENSG00000075624	Chromatin interaction
ENSG00000234432	Chromatin interaction
ENSG00000263900	Chromatin interaction
ENSG00000273084	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
5	nsv823996	chr7:5285503-5465988	Flanking Active TSS Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv887396	chr7:5305297-5475409	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	333 gene(s)	inside rSNPs	diseases
8	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
9	nsv533965	chr7:5370746-5548397	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
10	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
11	nsv887401	chr7:5393243-5539958	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
12	nsv887402	chr7:5394951-5494677	Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
14	nsv887405	chr7:5409059-5552436	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
15	nsv887406	chr7:5414602-5552436	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
16	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
17	nsv887407	chr7:5432672-5605130	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	302 gene(s)	inside rSNPs	diseases
18	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
19	nsv508443	chr7:5447283-5501122	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
20	nsv526194	chr7:5452756-5592436	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	278 gene(s)	inside rSNPs	diseases
21	nsv823997	chr7:5457916-5463961	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 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	chr7:5453200-5458600	Weak transcription	Aorta	Aorta
2	chr7:5456400-5458600	Enhancers	Placenta	Placenta
3	chr7:5456800-5458600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:5456800-5458800	Enhancers	Fetal Heart	heart
5	chr7:5457000-5458600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:5457000-5458600	Flanking Active TSS	Fetal Brain Female	brain
7	chr7:5457000-5459000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:5457000-5459400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr7:5457000-5461400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:5457200-5458600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:5457200-5458600	Enhancers	Small Intestine	intestine
12	chr7:5457200-5458800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:5457200-5458800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr7:5457200-5458800	Flanking Active TSS	NHDF-Ad	bronchial
15	chr7:5457200-5459200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr7:5457200-5459400	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr7:5457200-5461000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
18	chr7:5457400-5458600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:5457400-5458600	Bivalent Enhancer	Fetal Thymus	thymus
20	chr7:5457400-5458800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:5457400-5459400	Flanking Active TSS	A549	lung
22	chr7:5457600-5458800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr7:5457600-5458800	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr7:5457600-5461000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:5457800-5458600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
26	chr7:5457800-5458600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr7:5457800-5458800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:5457800-5458800	Bivalent Enhancer	Primary B cells from cord blood	blood
29	chr7:5457800-5458800	Flanking Active TSS	Fetal Brain Male	brain
30	chr7:5457800-5458800	Flanking Active TSS	Stomach Mucosa	stomach
31	chr7:5457800-5459000	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr7:5457800-5459200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
33	chr7:5457800-5459200	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr7:5457800-5459200	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr7:5457800-5459600	Flanking Active TSS	Hela-S3	cervix
36	chr7:5457800-5459800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr7:5457800-5461400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:5458000-5458600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:5458000-5458600	Flanking Active TSS	Fetal Kidney	kidney
40	chr7:5458000-5458800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr7:5458000-5458800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr7:5458000-5459000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr7:5458000-5459000	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr7:5458000-5459000	Flanking Active TSS	Ovary	ovary
45	chr7:5458000-5459000	Flanking Active TSS	HSMM	muscle
46	chr7:5458000-5459000	Flanking Active TSS	K562	blood
47	chr7:5458000-5459200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
48	chr7:5458000-5459200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
49	chr7:5458000-5459200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:5458000-5459200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links