Variant report

Variant	esv3398295
Chromosome Location	chr7:2887626-2892424
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr7:2890310-2890341	K562	blood:	n/a	n/a
2	BATF	chr7:2891103-2891348	GM12878	blood:	n/a	n/a
3	BATF	chr7:2891089-2891445	GM12878	blood:	n/a	n/a
4	CTCF	chr7:2887580-2887730	HepG2	liver:	n/a	n/a
5	CTCF	chr7:2891200-2891350	AG04450	lung:	n/a	n/a
6	CTCF	chr7:2887520-2887670	Caco-2	colon:	n/a	n/a
7	CTCF	chr7:2891300-2891450	GM06990	blood:	n/a	n/a
8	CTCF	chr7:2891340-2891490	GM12871	blood:	n/a	n/a
9	CTCF	chr7:2891285-2891393	GM12878	blood:	n/a	n/a
10	CTCF	chr7:2891220-2891370	HCFaa	heart:	n/a	n/a
11	CTCF	chr7:2891220-2891370	AoAF	blood vessel:	n/a	n/a
12	CTCF	chr7:2889829-2890420	GM19239	blood:	n/a	n/a
13	CTCF	chr7:2889649-2889828	GM19239	blood:	n/a	n/a
14	CTCF	chr7:2891220-2891370	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr7:2891280-2891430	HPAF	blood vessel:	n/a	n/a
16	EBF1	chr7:2891146-2891390	GM12878	blood:	n/a	n/a
17	EP300	chr7:2891103-2891397	GM12878	blood:	n/a	n/a
18	GATA2	chr7:2889682-2890514	K562	blood:	n/a	n/a
19	MAFF	chr7:2891248-2891257	K562	blood:	n/a	n/a
20	NFIC	chr7:2890955-2891436	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:2889851-2890111	Gliobla	brain:	n/a	n/a
22	POLR2A	chr7:2890978-2891000	MCF10A-Er-Src	breast:	n/a	n/a
23	RCOR1	chr7:2890102-2890281	K562	blood:	n/a	n/a
24	RUNX3	chr7:2891078-2891487	GM12878	blood:	n/a	n/a
25	RUNX3	chr7:2890975-2891555	GM12878	blood:	n/a	n/a
26	SUZ12	chr7:2889668-2890483	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF12	chr7:2890085-2890542	HepG2	liver:	n/a	n/a
28	TCF12	chr7:2891233-2891408	GM12878	blood:	n/a	n/a
29	ZNF143	chr7:2891295-2891364	GM12878	blood:	n/a	n/a
30	ZNF384	chr7:2890796-2891444	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:2887873-2887923	HL-60	blood:	n/a
2	chr7:2887873-2887923	NB4	blood:	n/a
3	chr7:2887873-2887923	ECC-1	luminal epithelium:	n/a
4	chr7:2887873-2887923	AG04450	lung:	fetal
5	chr7:2887873-2887923	PrEC	prostate:	n/a
6	chr7:2887873-2887923	HepG2	liver:	n/a
7	chr7:2887873-2887923	HCT-116	colon:	n/a
8	chr7:2887873-2887923	AG10803	skin:	n/a
9	chr7:2887873-2887923	MCF10A-Er-Src	breast:	n/a
10	chr7:2887873-2887923	SK-N-SH	brain:	n/a
11	chr7:2887873-2887923	SK-N-SH_RA	brain:	n/a
12	chr7:2887873-2887923	IMR90	lung:	fetal
13	chr7:2887873-2887923	SAEC	small airway:	n/a
14	chr7:2887873-2887923	GM12878	blood:	n/a
15	chr7:2887873-2887923	HEEpiC	esophagus:	n/a
16	chr7:2887873-2887923	HRPEpiC	eye:	n/a
17	chr7:2887873-2887923	BJ	skin:	n/a
18	chr7:2887873-2887923	HRCEpiC	kidney:	n/a
19	chr7:2887873-2887923	Jurkat	blood:	n/a
20	chr7:2887873-2887923	SKMC	muscle:	n/a
21	chr7:2887873-2887923	HRE	kidney:	n/a
22	chr7:2887873-2887923	H1-hESC	embryonic stem cell:	embryo
23	chr7:2887873-2887923	GM06990	blood:	n/a
24	chr7:2887873-2887923	GM12891	blood:	n/a
25	chr7:2887873-2887923	ProgFib	skin:	n/a
26	chr7:2887873-2887923	AG04449	skin:	fetal
27	chr7:2887873-2887923	LNCaP	prostate:	n/a
28	chr7:2887873-2887923	AoSMC	blood vessel:	n/a
29	chr7:2887873-2887923	NHDF-neo	bronchial:	n/a
30	chr7:2887873-2887923	U87	brain:	n/a
31	chr7:2887873-2887923	MCF-7	breast:	n/a
32	chr7:2887873-2887923	HUVEC	blood vessel:	n/a
33	chr7:2887873-2887923	BE2_C	brain:	n/a
34	chr7:2887873-2887923	RPTEC	kidney:	n/a
35	chr7:2887873-2887923	T-47D	breast:	n/a
36	chr7:2887873-2887923	AG09319	gingival:	n/a
37	chr7:2887873-2887923	NT2-D1	testis:	n/a
38	chr7:2887873-2887923	GM19239	blood:	n/a
39	chr7:2887873-2887923	PFSK-1	brain:	n/a
40	chr7:2887873-2887923	NH-A	brain:	n/a
41	chr7:2887873-2887923	K562	blood:	n/a
42	chr7:2887873-2887923	CMK	blood:	n/a
43	chr7:2887873-2887923	HCM	heart:	n/a
44	chr7:2887873-2887923	SK-N-MC	brain:	n/a
45	chr7:2887873-2887923	HCPEpiC	choroid plexus:	n/a
46	chr7:2887873-2887923	Hepatocyte	liver:	n/a
47	chr7:2887873-2887923	GM12892	blood:	n/a
48	chr7:2887873-2887923	NHBE	bronchial:	n/a
49	chr7:2887873-2887923	HCF	heart:	n/a
50	chr7:2887873-2887923	HNPCEpiC	eye:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:2891216..2892935-chr7:2895055..2897737,2	K562	blood:
2	chr7:2847142..2848969-chr7:2888487..2890440,2	MCF-7	breast:
3	chr7:2882956..2885508-chr7:2891694..2894640,3	MCF-7	breast:
4	chr7:2890202..2892822-chr7:2894073..2897035,2	MCF-7	breast:
5	chr7:2882986..2886273-chr7:2886531..2891062,6	MCF-7	breast:
6	chr7:2873423..2874992-chr7:2887430..2888992,2	MCF-7	breast:

No data

Variant related genes	Relation type
GNA12	TF binding region
GNA12	CpG island
ENSG00000146535	chromatin interactions

Extended variants
information (count: 211 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:211 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553987169	chr7:2887748-2887749	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs567611005	chr7:2887754-2887755	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs11768001	chr7:2887783-2887784	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs142957769	chr7:2887789-2887790	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs368127888	chr7:2887836-2887837	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs575544485	chr7:2887849-2887850	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs145958255	chr7:2887873-2887874	Weak transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs576423605	chr7:2887874-2887875	Weak transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs185364734	chr7:2887900-2887901	Weak transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs188188239	chr7:2887946-2887947	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs76111556	chr7:2887958-2887959	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs543260166	chr7:2887959-2887960	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs562367008	chr7:2887971-2887972	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs139875636	chr7:2887978-2887979	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs11770451	chr7:2887990-2887991	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs35637752	chr7:2888014-2888015	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs11768054	chr7:2888015-2888016	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs1614791	chr7:2888057-2888058	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs183667484	chr7:2888087-2888088	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs188374550	chr7:2888128-2888129	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs541239878	chr7:2888146-2888147	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs181777211	chr7:2888185-2888186	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs569837921	chr7:2888204-2888205	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs538268602	chr7:2888225-2888226	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs185719049	chr7:2888232-2888233	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs577758140	chr7:2888233-2888234	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs149659702	chr7:2888277-2888278	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs553949652	chr7:2888278-2888279	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs574149451	chr7:2888282-2888283	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs541872623	chr7:2888312-2888313	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs190544517	chr7:2888337-2888338	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs181853540	chr7:2888409-2888410	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs145476885	chr7:2888418-2888419	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs148477932	chr7:2888440-2888441	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs533325100	chr7:2888458-2888459	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs186883091	chr7:2888520-2888521	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs376065504	chr7:2888526-2888527	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs142735817	chr7:2888528-2888529	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs527388945	chr7:2888553-2888554	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs547467376	chr7:2888646-2888647	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs567368307	chr7:2888658-2888659	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs529936601	chr7:2888694-2888695	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs190034665	chr7:2888722-2888723	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs111695928	chr7:2888734-2888735	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs75803282	chr7:2888799-2888800	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs147614199	chr7:2888800-2888801	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs571261372	chr7:2888805-2888806	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs181246924	chr7:2888814-2888815	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs553816443	chr7:2888825-2888826	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs146116133	chr7:2888845-2888846	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Chordoma	21602918	CNVD
Lynch syndrome	22585707	CNVD
Follicular lymphoma	20505157	CNVD
Breast cancer	16397240	CNVD
Raine Syndrome	17924334	CNVD
Diffuse large b-cell lymphoma	21266526	CNVD
Melanoma	18172304	CNVD
Sudden cardiac death	19188705	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	16573809	CNVD
Glioma	18556773	CNVD
Ovarian cancer	21720365	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Ovarian cancer	22174824	CNVD
Urothelial carcinoma	18382360	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Biliary cancer	19435499	CNVD
Cancer	16751803	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	17387387	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	18923191	CNVD
Glioma	21971842	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
colon cancer	17210682	CNVD
Lung adenocarcinoma	21810691	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Colorectal cancer	19359472	CNVD
Hypothalamic hamartomas	18252217	CNVD
Human rectal carcinomas	16397240	CNVD
Peripheral t-cell lymphoma	19118030	CNVD
Medulloblastoma	18056178	CNVD
Basal cell lymphoma	17170743	CNVD
Ewing''s sarcoma	21437220	CNVD
Thyroid cancer	19087340	CNVD
Seminomas	18059402	CNVD
Testicular cancer	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	19415332	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
T-cell lymphomas	19863542	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
head and neck squamous cell carcinoma	19289630	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
Developmental delay	21147756	CNVD
Prostate cancer	18632612	CNVD
Urothelial carcinoma	21177765	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21509527	CNVD
Nasopharyngeal cancer	20548289	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Leukemia	23979775	CNVD
Spondylocostal dysostosis	21085971	CNVD
Mental retardation	17901693	CNVD
Heart disease	21282601	CNVD
Glioblastoma multiforme	22286061	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	17053054	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2884600-2889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:2884600-2889600	Weak transcription	Fetal Kidney	kidney
3	chr7:2884600-2896000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:2884600-2902800	Weak transcription	Right Ventricle	heart
5	chr7:2884800-2887800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr7:2884800-2887800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:2884800-2889600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:2884800-2889800	Weak transcription	Fetal Brain Male	brain
9	chr7:2884800-2889800	Weak transcription	Pancreas	Pancrea
10	chr7:2884800-2890600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:2884800-2891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:2884800-2891200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:2884800-2891200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:2884800-2895800	Weak transcription	Fetal Heart	heart
15	chr7:2885000-2889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:2885000-2889800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr7:2885000-2890400	Weak transcription	Dnd41	blood
18	chr7:2885000-2891000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr7:2885000-2902000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr7:2886600-2887800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr7:2886600-2888000	Enhancers	Fetal Intestine Small	intestine
22	chr7:2887800-2888000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr7:2889600-2889800	Active TSS	Spleen	Spleen
24	chr7:2889600-2890400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:2889600-2890400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:2889600-2890400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
27	chr7:2889600-2890400	ZNF genes & repeats	Fetal Kidney	kidney
28	chr7:2889800-2890000	Flanking Active TSS	Spleen	Spleen
29	chr7:2889800-2890200	ZNF genes & repeats	Fetal Brain Male	brain
30	chr7:2889800-2890400	ZNF genes & repeats	Pancreas	Pancrea
31	chr7:2890000-2890600	Active TSS	Spleen	Spleen
32	chr7:2890000-2891000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:2890200-2890400	Enhancers	Gastric	stomach
34	chr7:2890400-2890600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:2890400-2890600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:2890400-2890800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr7:2890400-2891000	Weak transcription	Gastric	stomach
38	chr7:2890400-2891400	Enhancers	Dnd41	blood
39	chr7:2890400-2895800	Weak transcription	Pancreas	Pancrea
40	chr7:2890400-2896400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:2890600-2891600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr7:2890600-2891800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:2891000-2891200	Active TSS	GM12878-XiMat	blood
44	chr7:2891000-2891200	Enhancers	NH-A	brain
45	chr7:2891000-2891200	Enhancers	NHDF-Ad	bronchial
46	chr7:2891000-2891400	Enhancers	Primary B cells from peripheral blood	blood
47	chr7:2891000-2891400	Enhancers	Osteobl	bone
48	chr7:2891000-2891600	Enhancers	Primary T cells from cord blood	blood
49	chr7:2891000-2891600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr7:2891000-2891600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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