Variant report

Variant	esv3506539
Chromosome Location	chr3:160232858-160236856
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:123)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:160236650-160236695	Kidney_OC	kidney:	n/a	n/a
2	FOS	chr3:160235224-160235418	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:160233254-160233361	K562	blood:	n/a	n/a
4	POLR2A	chr3:160233738-160233950	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:160233218-160233423	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:160233236-160233248	K562	blood:	n/a	n/a
7	POLR2A	chr3:160236486-160236654	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:160235047-160235082	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:160234859-160235108	A549	lung:	n/a	n/a
10	POLR2A	chr3:160235151-160235229	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:160233360-160233496	MCF-7	breast:	n/a	n/a
12	POLR2A	chr3:160234775-160235470	K562	blood:	n/a	n/a
13	POLR2A	chr3:160235065-160235131	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:160234252-160234408	Hela-S3	cervix:	n/a	n/a
15	STAT3	chr3:160233234-160233392	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF7L2	chr3:160234341-160234464	Hela-S3	cervix:	n/a	n/a

(count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:160233563-160233613	BJ	skin:	n/a
2	chr3:160233563-160233613	BJ	skin:	n/a
3	chr3:160233563-160233613	HRCEpiC	kidney:	n/a
4	chr3:160233797-160233847	HRCEpiC	kidney:	n/a
5	chr3:160233797-160233847	HEK293	kidney:	embryo
6	chr3:160233797-160233847	Caco-2	colon:	n/a
7	chr3:160233563-160233613	SK-N-SH_RA	brain:	n/a
8	chr3:160233563-160233613	Jurkat	blood:	n/a
9	chr3:160233797-160233847	HNPCEpiC	eye:	n/a
10	chr3:160233797-160233847	PANC-1	pancreas:	n/a
11	chr3:160233563-160233613	PrEC	prostate:	n/a
12	chr3:160233563-160233613	Hela-S3	cervix:	n/a
13	chr3:160233563-160233613	GM12892	blood:	n/a
14	chr3:160233797-160233847	NHDF-neo	bronchial:	n/a
15	chr3:160233797-160233847	HIPEpiC	eye:	n/a
16	chr3:160233797-160233847	SK-N-MC	brain:	n/a
17	chr3:160233563-160233613	MCF10A-Er-Src	breast:	n/a
18	chr3:160233797-160233847	LNCaP	prostate:	n/a
19	chr3:160233797-160233847	K562	blood:	n/a
20	chr3:160233563-160233613	K562	blood:	n/a
21	chr3:160233563-160233613	SK-N-MC	brain:	n/a
22	chr3:160233797-160233847	HMEC	breast:	n/a
23	chr3:160233797-160233847	NB4	blood:	n/a
24	chr3:160233563-160233613	GM12878	blood:	n/a
25	chr3:160233563-160233613	AG10803	skin:	n/a
26	chr3:160233563-160233613	HCF	heart:	n/a
27	chr3:160233797-160233847	Hela-S3	cervix:	n/a
28	chr3:160233797-160233847	AG10803	skin:	n/a
29	chr3:160233563-160233613	HIPEpiC	eye:	n/a
30	chr3:160233797-160233847	IMR90	lung:	fetal
31	chr3:160233797-160233847	HepG2	liver:	n/a
32	chr3:160233797-160233847	PrEC	prostate:	n/a
33	chr3:160233563-160233613	SAEC	small airway:	n/a
34	chr3:160233797-160233847	GM06990	blood:	n/a
35	chr3:160233563-160233613	HL-60	blood:	n/a
36	chr3:160233563-160233613	SK-N-SH	brain:	n/a
37	chr3:160233563-160233613	BE2_C	brain:	n/a
38	chr3:160233797-160233847	GM19239	blood:	n/a
39	chr3:160233797-160233847	T-47D	breast:	n/a
40	chr3:160233563-160233613	T-47D	breast:	n/a
41	chr3:160233797-160233847	NT2-D1	testis:	n/a
42	chr3:160233563-160233613	HMEC	breast:	n/a
43	chr3:160233563-160233613	SKMC	muscle:	n/a
44	chr3:160233563-160233613	LNCaP	prostate:	n/a
45	chr3:160233563-160233613	HUVEC	blood vessel:	n/a
46	chr3:160233797-160233847	SK-N-SH_RA	brain:	n/a
47	chr3:160233797-160233847	GM12891	blood:	n/a
48	chr3:160233563-160233613	NHBE	bronchial:	n/a
49	chr3:160233797-160233847	HAEpiC	amniotic membrane:	n/a
50	chr3:160233797-160233847	U87	brain:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160167035..160169821-chr3:160232708..160234646,2	K562	blood:
2	chr3:160220685..160224773-chr3:160234023..160237053,3	MCF-7	breast:
3	chr3:160223761..160225418-chr3:160235399..160237999,2	K562	blood:
4	chr3:160230934..160232886-chr3:160280729..160283145,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM59-2	chr3:160232695-160233024	NONHSAT092997

No data

Variant related genes	Relation type
SCARNA7	TF binding region
SCARNA7	CpG island
ENSG00000213186	chromatin interactions

Extended variants
information (count: 160 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:160 , 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	rs533238679	chr3:160232880-160232881	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs140676844	chr3:160232887-160232888	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs376069434	chr3:160232928-160232929	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs551526582	chr3:160232954-160232955	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs3836374	chr3:160232961-160232962	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs180777154	chr3:160232966-160232967	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs549475191	chr3:160233010-160233011	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs112043538	chr3:160233019-160233020	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs557690504	chr3:160233062-160233063	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs553740301	chr3:160233093-160233094	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs56124988	chr3:160233154-160233155	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs374433810	chr3:160233191-160233192	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs186019691	chr3:160233211-160233212	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs199644392	chr3:160233225-160233226	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs201026574	chr3:160233320-160233321	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs1803012	chr3:160233322-160233323	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs200620313	chr3:160233345-160233346	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs191237821	chr3:160233396-160233397	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs199571359	chr3:160233400-160233401	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs114801599	chr3:160233404-160233405	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs112603907	chr3:160233407-160233408	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs565055004	chr3:160233412-160233413	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs561303211	chr3:160233435-160233436	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs572265626	chr3:160233474-160233475	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs377257147	chr3:160233530-160233531	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs541229508	chr3:160233561-160233562	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs377338059	chr3:160233564-160233565	Weak transcription Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs182985644	chr3:160233584-160233585	Weak transcription Strong transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs543793964	chr3:160233678-160233679	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs145301883	chr3:160233685-160233686	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs535544725	chr3:160233691-160233692	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs551459306	chr3:160233751-160233752	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs117397315	chr3:160233755-160233756	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs527432334	chr3:160233783-160233784	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs374596478	chr3:160233797-160233798	Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs567384906	chr3:160233862-160233863	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs540965725	chr3:160233877-160233878	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs556207273	chr3:160233878-160233879	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs572525670	chr3:160233920-160233921	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs147628825	chr3:160233921-160233922	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs569910520	chr3:160233950-160233951	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs377229190	chr3:160233981-160233982	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs558580679	chr3:160233986-160233987	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs572203978	chr3:160233999-160234000	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs371248712	chr3:160234002-160234003	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs113452603	chr3:160234043-160234044	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs555127902	chr3:160234045-160234046	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs532740544	chr3:160234049-160234050	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs574959868	chr3:160234060-160234061	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs544064122	chr3:160234069-160234070	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

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	22032731	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
head and neck squamous cell carcinoma	17671120	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Basal cell lymphoma	17170743	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21364760	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Effusion lymphoma	18079361	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Bladder cancer	21909424	CNVD
Myelofibrosis	22110671	CNVD
Cancer	20164919	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:211 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
2	chr3:160215600-160254200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:160215800-160254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160215800-160254200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:160215800-160254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:160216000-160254200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:160216200-160249200	Strong transcription	Liver	Liver
8	chr3:160216200-160254200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:160216400-160254400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:160216800-160253800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:160217200-160254000	Strong transcription	Dnd41	blood
12	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:160217800-160235000	Weak transcription	Fetal Brain Male	brain
14	chr3:160218800-160244800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:160219600-160233400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:160219800-160242200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
18	chr3:160220600-160246200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
20	chr3:160221600-160249000	Strong transcription	HUVEC	blood vessel
21	chr3:160222200-160244600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:160223400-160243000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:160224400-160233200	Weak transcription	Gastric	stomach
24	chr3:160224400-160233200	Weak transcription	Lung	lung
25	chr3:160225600-160259800	Weak transcription	Stomach Mucosa	stomach
26	chr3:160225800-160236800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:160226000-160233400	Strong transcription	Hela-S3	cervix
28	chr3:160226000-160235000	Weak transcription	Fetal Heart	heart
29	chr3:160226000-160244000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:160227000-160233200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:160227000-160234800	Weak transcription	Psoas Muscle	Psoas
32	chr3:160227200-160233200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:160227200-160234000	Weak transcription	Esophagus	oesophagus
34	chr3:160227200-160234800	Weak transcription	NHLF	lung
35	chr3:160227200-160238600	Weak transcription	Brain Angular Gyrus	brain
36	chr3:160227200-160238800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:160227400-160233200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:160227400-160238600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:160227800-160236200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:160229000-160233400	Weak transcription	Fetal Intestine Small	intestine
41	chr3:160229000-160253400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:160229200-160239000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:160229200-160247000	Strong transcription	Adipose Nuclei	Adipose
44	chr3:160229200-160252800	Strong transcription	Fetal Thymus	thymus
45	chr3:160229200-160253400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:160229200-160253400	Strong transcription	Osteobl	bone
47	chr3:160229200-160253600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:160229200-160254000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:160229200-160254000	Strong transcription	Placenta	Placenta
50	chr3:160229400-160237200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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