Variant report

Variant	nsv523529
Chromosome Location	chr3:143215472-143229569
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	CTCF	chr3:143223078-143223097	Lung_OC	lung:	n/a	n/a
2	CTCF	chr3:143223099-143223134	Lung_OC	lung:	n/a	n/a
3	FOS	chr3:143229496-143229715	MCF10A-Er-Src	breast:	n/a	chr3:143229620-143229631 chr3:143229624-143229633
4	FOS	chr3:143228189-143228247	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:143229557-143229782	MCF10A-Er-Src	breast:	n/a	chr3:143229620-143229631 chr3:143229624-143229633
6	FOS	chr3:143227093-143227380	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr3:143227062-143227391	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr3:143229563-143229710	MCF10A-Er-Src	breast:	n/a	chr3:143229620-143229631 chr3:143229624-143229633
9	FOS	chr3:143226966-143227362	MCF10A-Er-Src	breast:	n/a	n/a
10	KAP1	chr3:143219553-143219863	K562	blood:	n/a	n/a
11	MAFK	chr3:143228705-143228872	HepG2	liver:	n/a	n/a
12	MAX	chr3:143226967-143227031	NB4	blood:	n/a	n/a
13	MYC	chr3:143222398-143222404	MCF-7	breast:	n/a	n/a
14	MYC	chr3:143222218-143222550	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr3:143226865-143227268	MCF10A-Er-Src	breast:	n/a	chr3:143227042-143227052 chr3:143227042-143227052
16	MYC	chr3:143227017-143227276	MCF10A-Er-Src	breast:	n/a	chr3:143227042-143227052 chr3:143227042-143227052
17	MYC	chr3:143222430-143222435	MCF-7	breast:	n/a	n/a
18	MYC	chr3:143222012-143222118	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:143217270-143217285	K562	blood:	n/a	n/a
20	POLR2A	chr3:143222285-143222318	A549	lung:	n/a	n/a
21	POLR2A	chr3:143222355-143222508	A549	lung:	n/a	n/a
22	POLR2A	chr3:143227158-143227358	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:143222487-143222509	MCF-7	breast:	n/a	n/a
24	POLR2A	chr3:143229376-143229460	K562	blood:	n/a	n/a
25	POLR2A	chr3:143225582-143225782	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:143227235-143227363	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:143218291-143218423	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr3:143222098-143222237	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:143222338-143222345	A549	lung:	n/a	n/a
30	POLR2A	chr3:143224013-143224182	K562	blood:	n/a	n/a
31	POLR2A	chr3:143222346-143222433	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:143218401-143218659	K562	blood:	n/a	n/a
33	POLR2A	chr3:143218713-143218856	MCF10A-Er-Src	breast:	n/a	n/a
34	RFX5	chr3:143218805-143218816	K562	blood:	n/a	n/a
35	SPI1	chr3:143225024-143225464	HL-60	blood:	n/a	n/a
36	SPI1	chr3:143225070-143225404	HL-60	blood:	n/a	n/a
37	STAT3	chr3:143219319-143219496	MCF10A-Er-Src	breast:	n/a	n/a
38	STAT3	chr3:143218816-143218900	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr3:143226860-143227023	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr3:143229008-143229192	MCF10A-Er-Src	breast:	n/a	n/a
41	STAT3	chr3:143227257-143227294	MCF10A-Er-Src	breast:	n/a	n/a
42	STAT3	chr3:143225801-143225865	MCF10A-Er-Src	breast:	n/a	n/a
43	STAT3	chr3:143227370-143227404	MCF10A-Er-Src	breast:	n/a	n/a
44	TEAD4	chr3:143216259-143216533	H1-hESC	embryonic stem cell:	n/a	n/a
45	TEAD4	chr3:143216266-143216635	H1-hESC	embryonic stem cell:	n/a	n/a
46	TEAD4	chr3:143216277-143216619	K562	blood:	n/a	n/a
47	TEAD4	chr3:143216198-143216642	K562	blood:	n/a	n/a
48	YY1	chr3:143216240-143216544	K562	blood:	n/a	chr3:143216436-143216448 chr3:143216414-143216426
49	YY1	chr3:143216236-143216560	SK-N-SH_RA	brain:	n/a	chr3:143216436-143216448 chr3:143216414-143216426
50	YY1	chr3:143216174-143216629	H1-hESC	embryonic stem cell:	n/a	chr3:143216436-143216448 chr3:143216414-143216426

No.	Distal block	Cell Line	Cell type
1	chr3:143187283..143189159-chr3:143216488..143218723,2	K562	blood:
2	chr3:143212932..143214521-chr3:143217945..143220851,2	MCF-7	breast:
3	chr3:143205251..143209634-chr3:143211909..143216344,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAQR9-6	chr3:143222117-143223115	NONHSAT092527

Variant related genes	Relation type
GAPDHP47	TF binding region

Extended variants
information (count: 464 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:464 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs838600	chr3:143215472-143215473	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs544805796	chr3:143215534-143215535	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs552874232	chr3:143215591-143215592	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs563484432	chr3:143215600-143215601	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs530637780	chr3:143215603-143215604	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs79781730	chr3:143215621-143215622	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs190006057	chr3:143215663-143215664	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs370058365	chr3:143215673-143215674	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs79626130	chr3:143215694-143215695	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs112256450	chr3:143215789-143215790	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs861418	chr3:143215794-143215795	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs563526276	chr3:143215809-143215810	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs370780742	chr3:143215811-143215812	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs551599694	chr3:143215820-143215821	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs570205194	chr3:143215829-143215830	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs191770042	chr3:143215831-143215832	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs556055529	chr3:143215847-143215848	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs540420944	chr3:143215882-143215883	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs574380765	chr3:143215933-143215934	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs73008894	chr3:143215968-143215969	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs183979654	chr3:143216000-143216001	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs137931824	chr3:143216023-143216024	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs189105962	chr3:143216155-143216156	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs563238863	chr3:143216186-143216187	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs553337587	chr3:143216213-143216214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs73008895	chr3:143216217-143216218	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs12633957	chr3:143216235-143216236	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs560795184	chr3:143216247-143216248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs528348664	chr3:143216446-143216447	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs149479021	chr3:143216565-143216566	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs559287806	chr3:143216582-143216583	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs533194741	chr3:143216624-143216625	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs143969213	chr3:143216734-143216735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs838601	chr3:143216783-143216784	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs181515560	chr3:143216812-143216813	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs71307940	chr3:143216818-143216819	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs75143927	chr3:143216825-143216826	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs577018626	chr3:143216840-143216841	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs114103486	chr3:143216844-143216845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs187591975	chr3:143216845-143216846	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs561381248	chr3:143216857-143216858	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs148661222	chr3:143216903-143216904	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs577516915	chr3:143216955-143216956	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs538263780	chr3:143216975-143216976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs556954738	chr3:143217026-143217027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs57446139	chr3:143217048-143217049	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs542734302	chr3:143217061-143217062	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs554327238	chr3:143217082-143217083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs190324540	chr3:143217099-143217100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs142837183	chr3:143217106-143217107	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

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
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
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Adrenocortical carcinoma	18281524	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:134 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143174400-143220400	Weak transcription	Fetal Lung	lung
2	chr3:143176800-143220400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:143179400-143220400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:143186000-143215600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:143186000-143223000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
7	chr3:143201800-143226400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:143209000-143226800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:143212600-143224800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:143212600-143247400	Weak transcription	Primary T cells from cord blood	blood
11	chr3:143214000-143216200	Enhancers	Colon Smooth Muscle	Colon
12	chr3:143214400-143215800	Enhancers	Rectal Smooth Muscle	rectum
13	chr3:143215200-143215600	Enhancers	Fetal Stomach	stomach
14	chr3:143215600-143226800	Weak transcription	Fetal Stomach	stomach
15	chr3:143219800-143222200	Weak transcription	Esophagus	oesophagus
16	chr3:143220200-143220800	Enhancers	Brain Angular Gyrus	brain
17	chr3:143220200-143220800	Enhancers	Brain Germinal Matrix	brain
18	chr3:143220200-143221200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:143220200-143221200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:143220200-143221200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:143220200-143221200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:143220400-143220800	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:143220400-143220800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:143220400-143221000	Enhancers	Brain Substantia Nigra	brain
25	chr3:143220400-143221200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:143220400-143221200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:143220400-143221200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:143220400-143221200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:143220400-143221200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:143220400-143221200	Enhancers	Brain Hippocampus Middle	brain
31	chr3:143220400-143221400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:143220400-143221800	Enhancers	Fetal Lung	lung
33	chr3:143220400-143226400	Weak transcription	HSMMtube	muscle
34	chr3:143220600-143220800	Enhancers	Brain Anterior Caudate	brain
35	chr3:143220600-143221200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:143220600-143221200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:143220800-143221200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr3:143220800-143221200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
39	chr3:143220800-143226600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:143221000-143222400	Weak transcription	Spleen	Spleen
41	chr3:143221000-143227200	Weak transcription	Brain Substantia Nigra	brain
42	chr3:143221200-143224000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:143221200-143226800	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:143221200-143228200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:143221400-143223800	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:143221400-143224600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:143221800-143222200	Weak transcription	Fetal Lung	lung
48	chr3:143222200-143222400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:143222200-143222600	Enhancers	Gastric	stomach
50	chr3:143222200-143222800	Strong transcription	Fetal Lung	lung

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