Variant report

Variant	nsv520488
Chromosome Location	chr3:69104752-69114005
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	chr3:69107820-69107890	Spleen_OC	spleen:	n/a	n/a
2	EBF1	chr3:69107615-69108044	GM12878	blood:	n/a	n/a
3	EBF1	chr3:69107646-69108027	GM12878	blood:	n/a	n/a
4	IKZF1	chr3:69107614-69107922	GM12878	blood:	n/a	n/a
5	IRF1	chr3:69105740-69105822	K562	blood:	n/a	n/a
6	MAFK	chr3:69112967-69113146	HepG2	liver:	n/a	n/a
7	MAX	chr3:69107590-69107995	NB4	blood:	n/a	chr3:69107748-69107758
8	MAX	chr3:69107598-69108017	GM12878	blood:	n/a	chr3:69107748-69107758
9	MYC	chr3:69107592-69108050	NB4	blood:	n/a	chr3:69107748-69107758
10	NFYB	chr3:69113243-69113433	GM12878	blood:	n/a	n/a
11	PAX5	chr3:69107688-69107924	GM12878	blood:	n/a	chr3:69107776-69107785
12	POLR2A	chr3:69109112-69109154	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr3:69107605-69108001	GM12892	blood:	n/a	n/a
14	POLR2A	chr3:69107601-69107990	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:69107798-69107971	ProgFib	skin:	n/a	n/a
16	POLR2A	chr3:69106139-69106161	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:69106108-69106308	K562	blood:	n/a	n/a
18	POLR2A	chr3:69106094-69106118	HepG2	liver:	n/a	n/a
19	REST	chr3:69107611-69107907	Hela-S3	cervix:	n/a	n/a
20	RUNX3	chr3:69107531-69107950	GM12878	blood:	n/a	n/a
21	RUNX3	chr3:69107567-69107939	GM12878	blood:	n/a	n/a
22	SPI1	chr3:69107572-69108004	GM12891	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
23	SPI1	chr3:69107612-69107975	GM12878	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
24	SPI1	chr3:69107563-69107997	HL-60	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
25	SPI1	chr3:69107672-69107839	K562	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
26	SPI1	chr3:69107568-69108053	GM12891	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
27	SPI1	chr3:69107485-69108069	HL-60	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
28	SPI1	chr3:69107469-69108156	GM12878	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
29	SPI1	chr3:69107605-69107865	GM12878	blood:	n/a	chr3:69107773-69107786 chr3:69107772-69107785
30	STAT3	chr3:69113382-69113500	MCF10A-Er-Src	breast:	n/a	n/a
31	ZNF143	chr3:69107686-69107821	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:69108232..69109950-chr3:69128693..69130790,2	MCF-7	breast:
2	chr3:69106718..69109466-chr3:69127570..69131265,3	K562	blood:
3	chr3:69100382..69102316-chr3:69105831..69107847,2	MCF-7	breast:
4	chr3:69106222..69108037-chr3:69127614..69129701,2	MCF-7	breast:
5	chr3:69105141..69107620-chr3:69110024..69112516,2	MCF-7	breast:
6	chr3:69100746..69102439-chr3:69110654..69113039,2	K562	blood:
7	chr3:69103862..69105538-chr3:69119692..69122200,2	K562	blood:
8	chr3:69110772..69113240-chr3:69126872..69131199,4	K562	blood:
9	chr3:69110122..69112933-chr3:69121991..69123834,2	K562	blood:
10	chr3:69112430..69115275-chr3:69125875..69130297,4	MCF-7	breast:
11	chr3:69101463..69103053-chr3:69103207..69105030,2	MCF-7	breast:
12	chr3:69109903..69113240-chr3:69128307..69131122,3	K562	blood:
13	chr3:69103145..69105538-chr3:69119692..69122647,2	K562	blood:
14	chr3:69108014..69110452-chr3:69134129..69136532,2	MCF-7	breast:
15	chr3:69101467..69102974-chr3:69106514..69108885,2	K562	blood:
16	chr3:69105141..69107620-chr3:69110024..69112516,2	MCF-7	breast:
17	chr3:69098841..69101567-chr3:69102319..69104982,3	K562	blood:
18	chr3:69099534..69103484-chr3:69106514..69109685,4	K562	blood:
19	chr3:69101460..69104533-chr3:69105331..69108214,3	MCF-7	breast:
20	chr3:69101388..69105202-chr3:69127247..69129843,5	MCF-7	breast:
21	chr3:69105444..69107005-chr3:69126154..69128272,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL6IP5-1	chr3:69105184-69105773	ENSG00000244513.2

Variant related genes	Relation type
TMF1	TF binding region
UBA3	TF binding region
ENSG00000144747	chromatin interactions
ENSG00000144746	chromatin interactions
ENSG00000144744	chromatin interactions

Extended variants
information (count: 377 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:377 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6549180	chr3:69104752-69104753	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs368472155	chr3:69104772-69104773	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs548806957	chr3:69104799-69104800	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs565549537	chr3:69104867-69104868	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs528225356	chr3:69104905-69104906	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs376205557	chr3:69104959-69104960	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs369468250	chr3:69104961-69104962	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs137972832	chr3:69105028-69105029	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs372032347	chr3:69105035-69105036	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs182961972	chr3:69105047-69105048	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs375395014	chr3:69105077-69105078	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs201986464	chr3:69105082-69105083	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs200427111	chr3:69105083-69105084	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs201478063	chr3:69105084-69105085	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs200218591	chr3:69105085-69105086	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs200598255	chr3:69105086-69105087	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs373917529	chr3:69105113-69105114	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs372967958	chr3:69105116-69105117	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs199673266	chr3:69105123-69105124	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs201460306	chr3:69105143-69105144	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs541576675	chr3:69105159-69105160	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs369198309	chr3:69105165-69105166	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs370923957	chr3:69105231-69105232	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs577647719	chr3:69105251-69105252	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs147522669	chr3:69105281-69105282	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs574524037	chr3:69105309-69105310	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs116189705	chr3:69105315-69105316	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs140550798	chr3:69105376-69105377	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs528819601	chr3:69105387-69105388	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs116154388	chr3:69105437-69105438	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs370983354	chr3:69105441-69105442	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs371002436	chr3:69105475-69105476	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs377252360	chr3:69105478-69105479	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs528285733	chr3:69105488-69105489	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs551531826	chr3:69105498-69105499	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs148560815	chr3:69105616-69105617	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs533455830	chr3:69105628-69105629	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs549964875	chr3:69105639-69105640	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs375580256	chr3:69105732-69105733	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs149648949	chr3:69105784-69105785	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs192895255	chr3:69105793-69105794	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs142903142	chr3:69105796-69105797	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs9823793	chr3:69105859-69105860	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs549711279	chr3:69105865-69105866	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs151173720	chr3:69105882-69105883	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs371881891	chr3:69105888-69105889	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs373934284	chr3:69105923-69105924	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs368164002	chr3:69105940-69105941	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs371912485	chr3:69105958-69105959	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs554134140	chr3:69105989-69105990	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Breast cancer	21509527	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Autism	22102821	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Prostate cancer	17217626	CNVD
Urothelial cell carcinoma	18451213	CNVD
Alzheimer''s disease	22166940	CNVD
Mental retardation	20848658	CNVD
Breast cancer	17142309	CNVD
Breast cancer	21364760	CNVD
lymphocytic leukemia	21291569	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	22522925	CNVD
Melanoma	20877625	CNVD
Cancer	20164919	CNVD

Chromatin state (count:452 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69101400-69127000	Weak transcription	Small Intestine	intestine
2	chr3:69101600-69109800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:69101800-69107800	Weak transcription	Gastric	stomach
4	chr3:69101800-69107800	Weak transcription	Ovary	ovary
5	chr3:69101800-69109800	Weak transcription	Lung	lung
6	chr3:69101800-69110600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:69101800-69128400	Weak transcription	Aorta	Aorta
8	chr3:69102000-69106800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:69102000-69107200	Weak transcription	Left Ventricle	heart
10	chr3:69102000-69107400	Weak transcription	Fetal Brain Male	brain
11	chr3:69102000-69107600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:69102000-69107600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:69102000-69107600	Weak transcription	Thymus	Thymus
14	chr3:69102000-69107800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:69102000-69107800	Weak transcription	Esophagus	oesophagus
16	chr3:69102000-69108000	Weak transcription	NHLF	lung
17	chr3:69102000-69109800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:69102000-69109800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:69102000-69109800	Weak transcription	Spleen	Spleen
20	chr3:69102000-69110400	Weak transcription	Colonic Mucosa	Colon
21	chr3:69102000-69113200	Strong transcription	HSMM	muscle
22	chr3:69102000-69128200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:69102000-69128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:69102200-69105200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:69102200-69105800	Weak transcription	Brain Substantia Nigra	brain
26	chr3:69102200-69106600	Weak transcription	Primary T cells from cord blood	blood
27	chr3:69102200-69107200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:69102200-69107600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:69102200-69107600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:69102200-69107600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:69102200-69107600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:69102200-69107600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:69102200-69107600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:69102200-69107600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:69102200-69107600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:69102200-69107600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:69102200-69107800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:69102200-69107800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:69102200-69107800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:69102200-69107800	Weak transcription	Brain Angular Gyrus	brain
41	chr3:69102200-69107800	Weak transcription	Fetal Heart	heart
42	chr3:69102200-69107800	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:69102200-69107800	Weak transcription	Fetal Stomach	stomach
44	chr3:69102200-69107800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:69102200-69107800	Weak transcription	Psoas Muscle	Psoas
46	chr3:69102200-69107800	Weak transcription	HSMMtube	muscle
47	chr3:69102200-69108000	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:69102200-69109800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:69102200-69109800	Weak transcription	Pancreas	Pancrea
50	chr3:69102200-69109800	Weak transcription	Right Ventricle	heart

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