Variant report

Variant	esv2596946
Chromosome Location	chr3:112466909-112468471
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	CCNT2	chr3:112466797-112467008	K562	blood:	n/a	n/a
2	E2F4	chr3:112467051-112467391	MCF10A-Er-Src	breast:	n/a	chr3:112467255-112467264
3	EP300	chr3:112467687-112467880	K562	blood:	n/a	n/a
4	FOS	chr3:112467253-112467817	MCF10A-Er-Src	breast:	n/a	chr3:112467256-112467265
5	FOS	chr3:112467340-112467794	MCF10A-Er-Src	breast:	n/a	n/a
6	FOSL2	chr3:112467616-112468009	A549	lung:	n/a	n/a
7	JUND	chr3:112467108-112467290	HepG2	liver:	n/a	chr3:112467256-112467265
8	JUND	chr3:112467310-112467914	K562	blood:	n/a	n/a
9	MAFF	chr3:112467714-112467914	K562	blood:	n/a	chr3:112467751-112467765
10	MAFK	chr3:112467658-112467859	K562	blood:	n/a	chr3:112467750-112467766 chr3:112467748-112467768 chr3:112467751-112467765
11	MAFK	chr3:112467358-112467878	IMR90	lung:	n/a	chr3:112467750-112467766 chr3:112467748-112467768 chr3:112467751-112467765
12	RCOR1	chr3:112467250-112467921	K562	blood:	n/a	n/a
13	STAT3	chr3:112467108-112467807	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr3:112467172-112467920	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr3:112467189-112467806	MCF10A-Er-Src	breast:	n/a	n/a
16	TAL1	chr3:112466602-112466928	K562	blood:	n/a	chr3:112466753-112466771

No.	Distal block	Cell Line	Cell type
1	chr3:112278451..112281169-chr3:112466155..112467753,2	K562	blood:
2	chr13:50509795..50512385-chr3:112464979..112467287,2	MCF-7	breast:
3	chr3:112465788..112467955-chr3:112468785..112471247,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD200R1L-1	chr3:112468078-112468166	NR_110017
2	lnc-CD200R1L-1	chr3:112468078-112468166	XLOC_003218

Variant related genes	Relation type
ENSG00000240893	TF binding region
ENSG00000138459	chromatin interactions
ENSG00000144848	chromatin interactions
ENSG00000123178	chromatin interactions

Extended variants
information (count: 52 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:52 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544353231	chr3:112466922-112466923	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs820557	chr3:112466948-112466949	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs532997733	chr3:112467003-112467004	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs546572706	chr3:112467018-112467019	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs74778099	chr3:112467104-112467105	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs76359825	chr3:112467105-112467106	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs76701468	chr3:112467106-112467107	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs367545243	chr3:112467137-112467138	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs192353178	chr3:112467152-112467153	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs540553008	chr3:112467181-112467182	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs7428881	chr3:112467191-112467192	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs1387020	chr3:112467307-112467308	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs112032208	chr3:112467402-112467403	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs201286336	chr3:112467405-112467406	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs202096552	chr3:112467406-112467407	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs201798354	chr3:112467700-112467701	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs200022086	chr3:112467703-112467704	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs200411960	chr3:112467705-112467706	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs58378753	chr3:112467711-112467712	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs56795243	chr3:112467712-112467713	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs181531830	chr3:112467828-112467829	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs115562492	chr3:112467862-112467863	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs562104636	chr3:112467865-112467866	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs539454364	chr3:112467974-112467975	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs553054264	chr3:112468005-112468006	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs528041226	chr3:112468008-112468009	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs187074503	chr3:112468024-112468025	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs573110019	chr3:112468032-112468033	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs535359990	chr3:112468035-112468036	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs555615666	chr3:112468039-112468040	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs16859996	chr3:112468047-112468048	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs544410780	chr3:112468078-112468079	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs564173181	chr3:112468105-112468106	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs191129821	chr3:112468121-112468122	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs183438030	chr3:112468127-112468128	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs540248072	chr3:112468154-112468155	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs559864767	chr3:112468183-112468184	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs528857021	chr3:112468187-112468188	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs62262927	chr3:112468202-112468203	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs150676808	chr3:112468228-112468229	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs57311206	chr3:112468238-112468239	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs60413948	chr3:112468261-112468262	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs555967850	chr3:112468263-112468264	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs58720537	chr3:112468281-112468282	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs570623538	chr3:112468296-112468297	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs539515661	chr3:112468302-112468303	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs534896752	chr3:112468303-112468304	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs186647809	chr3:112468381-112468382	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs189541962	chr3:112468400-112468401	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs139984283	chr3:112468419-112468420	Weak transcription Enhancers	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
Hirschsprung''s Disease	21712996	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
Prostate cancer	21965145	CNVD
Cancer	21129771	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
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Basal cell lymphoma	21115979	CNVD
Attention deficit hyperactivity disorder	22180640	CNVD

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112458400-112467800	Weak transcription	Stomach Mucosa	stomach
2	chr3:112458800-112467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:112459000-112467000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:112459000-112470600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:112459200-112467800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:112462600-112468000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:112464200-112468000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:112464200-112469200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:112464400-112469200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:112464400-112470800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:112465000-112467000	Weak transcription	GM12878-XiMat	blood
12	chr3:112465000-112469200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:112465000-112469400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:112465400-112468200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr3:112465600-112467400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr3:112465800-112467800	Weak transcription	HMEC	breast
17	chr3:112465800-112468000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:112465800-112470800	Weak transcription	NHDF-Ad	bronchial
19	chr3:112466000-112467200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:112466000-112467200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:112466000-112467600	Enhancers	A549	lung
22	chr3:112466000-112468000	Enhancers	K562	blood
23	chr3:112466000-112469200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:112466200-112470400	Weak transcription	NH-A	brain
25	chr3:112466200-112470400	Weak transcription	Osteobl	bone
26	chr3:112466400-112467000	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:112466400-112467200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:112466600-112468000	Weak transcription	Placenta	Placenta
29	chr3:112466800-112467200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:112467000-112467200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:112467000-112467400	Enhancers	GM12878-XiMat	blood
32	chr3:112467000-112468600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr3:112467000-112470800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:112467200-112467400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112467200-112467400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:112467200-112467400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:112467200-112467600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:112467200-112468000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:112467200-112469400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:112467400-112467800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:112467400-112467800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:112467400-112468000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:112467600-112468000	Flanking Active TSS	A549	lung
44	chr3:112467600-112468200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:112467800-112468000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:112467800-112468000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr3:112467800-112468200	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr3:112467800-112468200	Enhancers	HMEC	breast
49	chr3:112467800-112468600	Enhancers	Stomach Mucosa	stomach
50	chr3:112468000-112468200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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