Variant report

Variant	esv3427207
Chromosome Location	chr3:142149962-142152010
allele	n/a
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	EBF1	chr3:142151996-142152029	GM12878	blood:	n/a	n/a
2	EP300	chr3:142151884-142152257	GM12878	blood:	n/a	n/a
3	GATA3	chr3:142151567-142151784	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr3:142151906-142151933	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr3:142151730-142152018	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142145904..142149296-chr3:142151128..142153785,4	K562	blood:
2	chr3:142145296..142147116-chr3:142150982..142153061,2	MCF-7	breast:
3	chr3:142145919..142149296-chr3:142150484..142152821,3	K562	blood:
4	chr3:142150817..142154662-chr3:142162783..142169338,6	MCF-7	breast:

Variant related genes	Relation type
XRN1	TF binding region
ENSG00000242479	chromatin interactions
ENSG00000114127	chromatin interactions

Extended variants
information (count: 98 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:98 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544242424	chr3:142149992-142149993	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs562487414	chr3:142150053-142150054	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs529779073	chr3:142150077-142150078	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs541900705	chr3:142150086-142150087	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs369776784	chr3:142150095-142150096	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs559952462	chr3:142150103-142150104	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs527882535	chr3:142150126-142150127	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs74985376	chr3:142150145-142150146	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs570827962	chr3:142150154-142150155	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs6781072	chr3:142150204-142150205	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs150049055	chr3:142150232-142150233	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs549937982	chr3:142150248-142150249	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs568441422	chr3:142150256-142150257	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs535613451	chr3:142150278-142150279	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs146166736	chr3:142150315-142150316	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs566130002	chr3:142150387-142150388	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs6768585	chr3:142150457-142150458	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs558750810	chr3:142150490-142150491	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs181334156	chr3:142150527-142150528	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs544495453	chr3:142150528-142150529	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs144005110	chr3:142150613-142150614	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs373083452	chr3:142150614-142150615	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs574384809	chr3:142150616-142150617	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs558175673	chr3:142150637-142150638	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs71153964	chr3:142150692-142150693	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs9848799	chr3:142150706-142150707	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs376867370	chr3:142150707-142150708	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs71750793	chr3:142150713-142150714	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs374051292	chr3:142150715-142150716	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs71304138	chr3:142150716-142150717	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs377215508	chr3:142150717-142150718	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs368206166	chr3:142150718-142150719	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs372469931	chr3:142150719-142150720	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs386398117	chr3:142150725-142150726	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs71153965	chr3:142150726-142150727	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs190662273	chr3:142150727-142150728	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs183036399	chr3:142150737-142150738	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs13061487	chr3:142150756-142150757	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs78945961	chr3:142150791-142150792	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs563227337	chr3:142150804-142150805	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs186569563	chr3:142150815-142150816	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs370370053	chr3:142150824-142150825	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs369848172	chr3:142150825-142150826	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs374053201	chr3:142150826-142150827	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs374924977	chr3:142150827-142150828	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs374379974	chr3:142150830-142150831	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs530755989	chr3:142150837-142150838	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs372710078	chr3:142150838-142150839	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs548961011	chr3:142150856-142150857	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs9835160	chr3:142150858-142150859	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:52)

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
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	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
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:234 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142083600-142158600	Weak transcription	NHEK	skin
2	chr3:142105000-142151800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:142106800-142150800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142112200-142151600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:142112200-142152000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:142112200-142152200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:142112200-142154600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:142112600-142150600	Strong transcription	Placenta	Placenta
9	chr3:142113000-142152200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:142114800-142151800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:142120400-142151800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:142120600-142151800	Strong transcription	Dnd41	blood
15	chr3:142125000-142151800	Strong transcription	Fetal Thymus	thymus
16	chr3:142127000-142152000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:142127200-142152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:142127400-142159600	Weak transcription	Psoas Muscle	Psoas
19	chr3:142131600-142156000	Weak transcription	Fetal Heart	heart
20	chr3:142134200-142152600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:142136400-142157400	Weak transcription	HMEC	breast
22	chr3:142136800-142150800	Strong transcription	Liver	Liver
23	chr3:142138600-142158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:142138600-142164600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:142138800-142163000	Weak transcription	Spleen	Spleen
26	chr3:142139200-142151200	Weak transcription	Right Ventricle	heart
27	chr3:142139400-142156200	Weak transcription	Small Intestine	intestine
28	chr3:142139400-142157000	Weak transcription	Brain Germinal Matrix	brain
29	chr3:142139400-142158600	Weak transcription	Pancreas	Pancrea
30	chr3:142139400-142163200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:142139600-142150400	Strong transcription	Primary hematopoietic stem cells	blood
32	chr3:142141200-142157000	Weak transcription	Esophagus	oesophagus
33	chr3:142141600-142162400	Weak transcription	Brain Angular Gyrus	brain
34	chr3:142142200-142151200	Weak transcription	Hela-S3	cervix
35	chr3:142142200-142165400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:142142400-142153400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:142142800-142153200	Weak transcription	HUVEC	blood vessel
38	chr3:142143600-142151800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:142144200-142151600	Strong transcription	Adipose Nuclei	Adipose
40	chr3:142144400-142150200	Strong transcription	Primary B cells from cord blood	blood
41	chr3:142145200-142150400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:142145800-142150400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:142145800-142151400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:142145800-142152200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr3:142146000-142150400	Strong transcription	Primary T cells from cord blood	blood
46	chr3:142146000-142150600	Strong transcription	Fetal Stomach	stomach
47	chr3:142146000-142151800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:142146200-142150400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:142146200-142151800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:142146400-142150200	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links