Variant report

Variant	esv3355546
Chromosome Location	chr3:141660462-141664660
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141456126..141457791-chr3:141659173..141662093,2	MCF-7	breast:
2	chr3:141662334..141665277-chr3:141666881..141671768,4	K562	blood:
3	chr3:141658582..141660731-chr3:141665381..141667726,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFDP2-5	chr3:141663270-141666233	ENSG00000269905.1

Variant related genes	Relation type
ENSG00000114125	chromatin interactions
ENSG00000269905	chromatin interactions

Extended variants
information (count: 170 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:170 , 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	rs555440601	chr3:141660511-141660512	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs567279114	chr3:141660595-141660596	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs535207445	chr3:141660620-141660621	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs532832817	chr3:141660623-141660624	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs10935446	chr3:141660655-141660656	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs10804681	chr3:141660675-141660676	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs183427079	chr3:141660728-141660729	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs12636926	chr3:141660742-141660743	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs542683589	chr3:141660756-141660757	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs377265737	chr3:141660757-141660758	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs561416393	chr3:141660826-141660827	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs74560446	chr3:141660835-141660836	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs528542160	chr3:141660836-141660837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs150972615	chr3:141660843-141660844	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs186862089	chr3:141660850-141660851	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs559076373	chr3:141660863-141660864	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs532969509	chr3:141660887-141660888	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs560852420	chr3:141660892-141660893	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs551252626	chr3:141660914-141660915	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs569664709	chr3:141660928-141660929	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs530506610	chr3:141660939-141660940	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs75865732	chr3:141660963-141660964	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs567272120	chr3:141660978-141660979	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs139062884	chr3:141660983-141660984	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs143996717	chr3:141661009-141661010	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs111434083	chr3:141661019-141661020	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs112989673	chr3:141661052-141661053	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs557664978	chr3:141661053-141661054	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs549408931	chr3:141661055-141661056	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs373464528	chr3:141661057-141661058	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs575881877	chr3:141661085-141661086	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs114823306	chr3:141661186-141661187	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs552643295	chr3:141661204-141661205	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs573195153	chr3:141661207-141661208	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs370718918	chr3:141661298-141661299	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs376738230	chr3:141661299-141661300	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs11347573	chr3:141661320-141661321	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs76115389	chr3:141661332-141661333	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs202052473	chr3:141661333-141661334	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs200234504	chr3:141661334-141661335	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs577415637	chr3:141661464-141661465	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs544835146	chr3:141661472-141661473	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs192108024	chr3:141661474-141661475	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs34051657	chr3:141661483-141661484	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs397699470	chr3:141661500-141661501	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs182790819	chr3:141661506-141661507	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs530684980	chr3:141661538-141661539	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs375650704	chr3:141661545-141661546	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs566019405	chr3:141661588-141661589	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs560678975	chr3:141661600-141661601	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:53)

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
T-cell prolymphocytic leukemia	17713554	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
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:150 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
2	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
6	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
8	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
9	chr3:141643000-141675800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:141643400-141671200	Weak transcription	Right Ventricle	heart
11	chr3:141644800-141678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:141646800-141668200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:141647000-141668400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:141647000-141669200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:141647200-141669400	Weak transcription	Primary B cells from cord blood	blood
16	chr3:141647400-141668200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:141647400-141670400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:141647600-141670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:141647800-141660800	Weak transcription	Lung	lung
20	chr3:141647800-141664200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:141647800-141668200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:141647800-141670200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:141648000-141660600	Weak transcription	Gastric	stomach
24	chr3:141648000-141664400	Weak transcription	Primary T cells from cord blood	blood
25	chr3:141648000-141670000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:141648000-141670800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:141648200-141663400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:141650000-141664200	Weak transcription	Dnd41	blood
29	chr3:141653200-141664400	Weak transcription	Fetal Stomach	stomach
30	chr3:141653400-141664200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:141656400-141660600	Enhancers	Fetal Brain Male	brain
32	chr3:141656600-141664400	Weak transcription	Esophagus	oesophagus
33	chr3:141656800-141660600	Weak transcription	K562	blood
34	chr3:141656800-141664200	Weak transcription	Thymus	Thymus
35	chr3:141657000-141660800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:141657000-141664600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:141658000-141661400	Enhancers	Fetal Intestine Large	intestine
38	chr3:141658600-141660800	Enhancers	Fetal Brain Female	brain
39	chr3:141658600-141660800	Enhancers	HUVEC	blood vessel
40	chr3:141658600-141661200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:141658800-141660800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:141658800-141661200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:141658800-141661200	Enhancers	Stomach Mucosa	stomach
44	chr3:141659000-141661000	Enhancers	Primary hematopoietic stem cells	blood
45	chr3:141659200-141660800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr3:141659200-141661000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:141659200-141696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:141659400-141661000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:141659400-141664000	Weak transcription	Fetal Thymus	thymus
50	chr3:141659400-141664400	Weak transcription	HSMMtube	muscle

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