Variant report

Variant	rs2029409
Chromosome Location	chr4:143316033-143316034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13126113	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1497387	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1906871	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2029410	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4956441	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6847867	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3324750	chr4:143315744-143316083	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3'	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143290400-143322000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:143300200-143326200	Weak transcription	Aorta	Aorta
3	chr4:143301200-143326200	Weak transcription	Gastric	stomach
4	chr4:143301400-143316200	Weak transcription	Dnd41	blood
5	chr4:143301600-143317400	Weak transcription	NH-A	brain
6	chr4:143301600-143322800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:143301600-143323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:143301600-143325400	Weak transcription	Left Ventricle	heart
9	chr4:143302200-143316400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:143302200-143323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:143305200-143321200	Weak transcription	HSMMtube	muscle
12	chr4:143306600-143320800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:143307200-143318800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr4:143307600-143320800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:143308200-143323200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:143309000-143323200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:143309000-143323400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:143309400-143317600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:143309400-143320600	Weak transcription	Primary T cells from cord blood	blood
20	chr4:143310000-143316600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr4:143310000-143317800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:143310200-143317400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:143312600-143320600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr4:143313000-143326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:143313200-143317200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:143313200-143317200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:143313400-143322800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:143314200-143316200	Weak transcription	NHDF-Ad	bronchial
29	chr4:143314600-143317000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:143314600-143317000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr4:143314600-143317200	Strong transcription	HMEC	breast
32	chr4:143314600-143318200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:143314800-143316600	Strong transcription	NHEK	skin
34	chr4:143315600-143316400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
35	chr4:143315600-143317800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:143315600-143318200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:143315800-143318600	Strong transcription	HSMM	muscle
38	chr4:143316000-143316400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:143316000-143316400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr4:143316000-143316400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:143316000-143316600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:143316000-143318600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:143316000-143323200	Weak transcription	Small Intestine	intestine

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