Variant report

Variant	esv3383963
Chromosome Location	chr4:2877954-2882252
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	FOS	chr4:2880201-2880240	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA2	chr4:2880108-2880511	HUVEC	blood vessel:	n/a	chr4:2880312-2880326
3	MAFF	chr4:2878751-2878917	HepG2	liver:	n/a	chr4:2878813-2878831
4	MAFK	chr4:2878782-2878895	IMR90	lung:	n/a	chr4:2878819-2878830 chr4:2878818-2878829 chr4:2878814-2878830 chr4:2878818-2878829 chr4:2878814-2878829 chr4:2878817-2878831 chr4:2878819-2878830
5	MAFK	chr4:2878735-2878971	HepG2	liver:	n/a	chr4:2878819-2878830 chr4:2878818-2878829 chr4:2878814-2878830 chr4:2878818-2878829 chr4:2878814-2878829 chr4:2878817-2878831 chr4:2878819-2878830
6	MAFK	chr4:2878743-2878953	HepG2	liver:	n/a	chr4:2878819-2878830 chr4:2878818-2878829 chr4:2878814-2878830 chr4:2878818-2878829 chr4:2878814-2878829 chr4:2878817-2878831 chr4:2878819-2878830
7	POLR2A	chr4:2882141-2882259	K562	blood:	n/a	n/a
8	POLR2A	chr4:2880087-2880304	K562	blood:	n/a	n/a
9	POLR2A	chr4:2880635-2880706	K562	blood:	n/a	n/a
10	POLR2A	chr4:2879187-2879289	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr4:2878659-2878757	HepG2	liver:	n/a	n/a
12	RAD21	chr4:2880230-2880254	IMR90	lung:	n/a	n/a
13	RCOR1	chr4:2880521-2880522	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:2818530..2821169-chr4:2881997..2885134,3	K562	blood:
2	chr4:2879534..2882793-chr4:2935370..2940285,4	MCF-7	breast:
3	chr4:2876022..2879054-chr4:2934409..2936795,3	MCF-7	breast:
4	chr4:2876464..2878755-chr4:2882679..2884281,2	K562	blood:
5	chr4:2868702..2870783-chr4:2881589..2883580,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3BP2-4	chr4:2878773-2878996	expReg_chr4_474_+
2	lnc-SH3BP2-3	chr4:2878344-2878589	expReg_chr4_472_+

Variant related genes	Relation type
ADD1	TF binding region
ENSG00000087274	chromatin interactions
ENSG00000087266	chromatin interactions
ENSG00000249673	chromatin interactions
ENSG00000109736	chromatin interactions

Extended variants
information (count: 189 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:189 , 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	rs558862821	chr4:2877956-2877957	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs577702415	chr4:2877991-2877992	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs567247854	chr4:2878037-2878038	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs16843523	chr4:2878074-2878075	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs563274879	chr4:2878075-2878076	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs528853124	chr4:2878079-2878080	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs549884234	chr4:2878084-2878085	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs144839741	chr4:2878129-2878130	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs542634983	chr4:2878138-2878139	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs559728486	chr4:2878159-2878160	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs76426949	chr4:2878169-2878170	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs75868344	chr4:2878194-2878195	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs75559060	chr4:2878212-2878213	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs111313934	chr4:2878239-2878240	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs76684461	chr4:2878245-2878246	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs376206366	chr4:2878246-2878247	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs528350513	chr4:2878247-2878248	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs79051134	chr4:2878280-2878281	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs551584263	chr4:2878289-2878290	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs79105750	chr4:2878299-2878300	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs77033114	chr4:2878321-2878322	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs76579600	chr4:2878330-2878331	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs80206452	chr4:2878332-2878333	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs77202826	chr4:2878333-2878334	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs79672655	chr4:2878351-2878352	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
26	rs571318521	chr4:2878355-2878356	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
27	rs149983001	chr4:2878364-2878365	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
28	rs77439795	chr4:2878365-2878366	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
29	rs74572753	chr4:2878372-2878373	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
30	rs550616245	chr4:2878426-2878427	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
31	rs567334991	chr4:2878448-2878449	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
32	rs188459542	chr4:2878453-2878454	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
33	rs552947218	chr4:2878482-2878483	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
34	rs567182399	chr4:2878490-2878491	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
35	rs538949141	chr4:2878498-2878499	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
36	rs559123016	chr4:2878513-2878514	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
37	rs567780310	chr4:2878565-2878566	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
38	rs561928678	chr4:2878566-2878567	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
39	rs35435678	chr4:2878579-2878580	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
40	rs180673417	chr4:2878637-2878638	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs376961329	chr4:2878678-2878679	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs575700832	chr4:2878720-2878721	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs569941709	chr4:2878729-2878730	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs397879163	chr4:2878745-2878746	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs562474744	chr4:2878746-2878747	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs61791180	chr4:2878749-2878750	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs77985186	chr4:2878763-2878764	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs557134341	chr4:2878777-2878778	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
49	rs573777618	chr4:2878784-2878785	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
50	rs542669709	chr4:2878790-2878791	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Facial dysmorphism	22438245	CNVD
Wolf-Hirschhorn syndrome	22438245	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:302 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2870600-2886000	Weak transcription	Fetal Brain Male	brain
3	chr4:2870800-2878800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:2871000-2885800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:2871200-2881600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:2871200-2886000	Weak transcription	Aorta	Aorta
7	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:2871400-2879400	Weak transcription	Gastric	stomach
10	chr4:2871600-2880800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:2871800-2880400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:2872200-2890800	Weak transcription	A549	lung
13	chr4:2873600-2878000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:2874000-2883600	Weak transcription	NH-A	brain
15	chr4:2874000-2887000	Weak transcription	Fetal Heart	heart
16	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
17	chr4:2874400-2880200	Weak transcription	HSMMtube	muscle
18	chr4:2874600-2878000	Enhancers	Brain Cingulate Gyrus	brain
19	chr4:2875000-2878800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:2875000-2879600	Weak transcription	Psoas Muscle	Psoas
21	chr4:2875000-2879800	Weak transcription	Spleen	Spleen
22	chr4:2875000-2880600	Weak transcription	Esophagus	oesophagus
23	chr4:2875400-2879600	Weak transcription	HUVEC	blood vessel
24	chr4:2875400-2880600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:2875400-2886000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:2875800-2878800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:2875800-2884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:2876000-2881800	Strong transcription	Fetal Intestine Small	intestine
29	chr4:2876000-2884000	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:2876000-2885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:2876000-2886000	Weak transcription	Colonic Mucosa	Colon
32	chr4:2876000-2886600	Weak transcription	Stomach Mucosa	stomach
33	chr4:2876400-2891600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:2876600-2882600	Strong transcription	Fetal Stomach	stomach
35	chr4:2876600-2889600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr4:2876800-2878000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:2876800-2881800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:2876800-2889000	Strong transcription	GM12878-XiMat	blood
40	chr4:2876800-2889400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:2876800-2891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:2877000-2878200	Strong transcription	HSMM	muscle
43	chr4:2877000-2882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:2877000-2882200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr4:2877000-2883600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:2877000-2883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:2877000-2886000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:2877000-2889800	Strong transcription	Dnd41	blood
49	chr4:2877200-2878200	Strong transcription	Primary B cells from cord blood	blood
50	chr4:2877200-2882000	Strong transcription	Brain Germinal Matrix	brain

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