Variant report

Variant	esv3461306
Chromosome Location	chr3:196054155-196058753
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr3:196057273-196057440	K562	blood:	n/a	n/a
2	FOXA1	chr3:196057526-196057829	HepG2	liver:	n/a	n/a
3	FOXA2	chr3:196057568-196057707	HepG2	liver:	n/a	n/a
4	IRF1	chr3:196055372-196055376	K562	blood:	n/a	n/a
5	POLR2A	chr3:196054276-196054621	A549	lung:	n/a	n/a
6	POLR2A	chr3:196055216-196055510	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:196054410-196054482	K562	blood:	n/a	n/a
8	POLR2A	chr3:196054324-196054391	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:196054423-196054600	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:196057167-196057257	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:196054398-196054482	MCF-7	breast:	n/a	n/a
12	POLR2A	chr3:196055687-196055695	K562	blood:	n/a	n/a
13	POLR2A	chr3:196054179-196054637	K562	blood:	n/a	n/a
14	POLR2A	chr3:196054193-196054497	K562	blood:	n/a	n/a
15	POLR2A	chr3:196054505-196054528	K562	blood:	n/a	n/a
16	POLR2A	chr3:196054175-196054746	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr3:196054485-196054493	MCF-7	breast:	n/a	n/a
18	POLR2A	chr3:196057521-196057705	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr3:196054264-196054549	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:196054170-196054608	K562	blood:	n/a	n/a
21	POLR2A	chr3:196054207-196054627	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196043658..196046454-chr3:196052736..196055681,2	MCF-7	breast:
2	chr3:196043597..196046565-chr3:196058227..196060990,3	K562	blood:
3	chr3:196049252..196052766-chr3:196054178..196057150,4	K562	blood:
4	chr3:196053196..196055442-chr3:196068574..196070294,2	MCF-7	breast:
5	chr3:196057685..196059203-chr3:196062080..196064140,2	MCF-7	breast:
6	chr3:196044943..196046563-chr3:196056014..196058811,2	MCF-7	breast:
7	chr3:196046919..196051231-chr3:196053241..196055569,4	K562	blood:
8	chr3:196039550..196042176-chr3:196054293..196056157,2	K562	blood:
9	chr3:196054872..196057138-chr3:196227517..196230475,2	K562	blood:
10	chr3:196047776..196049836-chr3:196051866..196054572,2	MCF-7	breast:
11	chr3:196054797..196056651-chr3:196089177..196091738,2	K562	blood:

No data

Variant related genes	Relation type
TM4SF19	TF binding region
ENSG00000145107	chromatin interactions
ENSG00000272741	chromatin interactions
ENSG00000235897	chromatin interactions
ENSG00000213123	chromatin interactions
ENSG00000212146	chromatin interactions

Extended variants
information (count: 165 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:165 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73212180	chr3:196054165-196054166	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs553861311	chr3:196054198-196054199	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs376674059	chr3:196054212-196054213	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
4	rs185711966	chr3:196054213-196054214	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
5	rs190191075	chr3:196054221-196054222	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
6	rs200291482	chr3:196054247-196054248	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
7	rs372533772	chr3:196054264-196054265	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
8	rs181068729	chr3:196054284-196054285	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
9	rs532304680	chr3:196054285-196054286	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
10	rs376328443	chr3:196054307-196054308	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
11	rs35783217	chr3:196054327-196054328	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
12	rs370709988	chr3:196054367-196054368	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
13	rs147419407	chr3:196054374-196054375	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
14	rs139779655	chr3:196054381-196054382	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
15	rs374081817	chr3:196054398-196054399	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
16	rs199859080	chr3:196054425-196054426	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
17	rs185911952	chr3:196054428-196054429	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
18	rs6785339	chr3:196054439-196054440	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs188688105	chr3:196054442-196054443	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs370162254	chr3:196054471-196054472	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs373508455	chr3:196054481-196054482	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
22	rs115080851	chr3:196054487-196054488	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
23	rs6782336	chr3:196054488-196054489	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs377222945	chr3:196054511-196054512	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
25	rs59016656	chr3:196054565-196054566	Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs115565690	chr3:196054673-196054674	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
27	rs116720607	chr3:196054682-196054683	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
28	rs535542699	chr3:196054738-196054739	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
29	rs138608700	chr3:196054800-196054801	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
30	rs572301747	chr3:196054807-196054808	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
31	rs6768240	chr3:196054822-196054823	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs558223565	chr3:196054827-196054828	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
33	rs541965312	chr3:196054831-196054832	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
34	rs78864681	chr3:196054835-196054836	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
35	rs36019671	chr3:196054847-196054848	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
36	rs6777819	chr3:196054860-196054861	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
37	rs562658919	chr3:196054873-196054874	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
38	rs551825001	chr3:196054890-196054891	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
39	rs574591415	chr3:196054948-196054949	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
40	rs376471672	chr3:196054963-196054964	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
41	rs370949107	chr3:196055000-196055001	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
42	rs541534375	chr3:196055022-196055023	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
43	rs560198537	chr3:196055028-196055029	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
44	rs111425549	chr3:196055106-196055107	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
45	rs554680176	chr3:196055170-196055171	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
46	rs143628089	chr3:196055206-196055207	Weak transcription Enhancers	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
47	rs181127056	chr3:196055343-196055344	Weak transcription Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
48	rs12636849	chr3:196055365-196055366	Weak transcription Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
49	rs185366261	chr3:196055424-196055425	Weak transcription Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
50	rs563764808	chr3:196055592-196055593	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Chronic lymphocytic leukemia	20421269	CNVD

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196045600-196054200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:196045600-196054200	Weak transcription	Ovary	ovary
3	chr3:196045800-196054200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:196046000-196054400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:196046200-196054200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:196047200-196054600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:196047400-196054200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:196047600-196054400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:196047600-196063600	Weak transcription	NHEK	skin
10	chr3:196051000-196057200	Weak transcription	Hela-S3	cervix
11	chr3:196051400-196063600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:196051600-196054200	Weak transcription	HSMMtube	muscle
13	chr3:196051800-196054800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:196052000-196062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:196053200-196054800	Strong transcription	K562	blood
16	chr3:196053600-196054800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:196053800-196054600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:196053800-196054800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:196054000-196054200	Enhancers	Fetal Stomach	stomach
20	chr3:196054000-196054400	Enhancers	Pancreas	Pancrea
21	chr3:196054000-196054400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
22	chr3:196054000-196054600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr3:196054000-196054600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:196054000-196054600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:196054000-196055600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:196054200-196054400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:196054200-196054400	Bivalent Enhancer	Fetal Stomach	stomach
28	chr3:196054200-196054400	Active TSS	Osteobl	bone
29	chr3:196054200-196054600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr3:196054200-196054600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:196054200-196054600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:196054200-196054600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:196054200-196054600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:196054200-196054600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr3:196054200-196054600	Enhancers	Ovary	ovary
36	chr3:196054200-196054800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr3:196054200-196054800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr3:196054200-196054800	Enhancers	HSMMtube	muscle
39	chr3:196054400-196054600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:196054400-196054600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:196054400-196054600	Enhancers	Osteobl	bone
42	chr3:196054400-196054800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:196054400-196054800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr3:196054400-196054800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:196054400-196054800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:196054400-196056400	Weak transcription	Pancreas	Pancrea
47	chr3:196054600-196054800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:196054600-196054800	Flanking Active TSS	Osteobl	bone
49	chr3:196054600-196061800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:196054600-196091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links