Variant report

Variant	rs1497401
Chromosome Location	chr4:143321490-143321491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143319256..143323277-chr4:143393099..143396432,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10006795	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10006884	0.86[AMR][1000 genomes]
rs10006971	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151359	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1982965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173208	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2322549	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62328321	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6812973	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6822835	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7696969	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

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	chr4:143301600-143322800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:143301600-143323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:143301600-143325400	Weak transcription	Left Ventricle	heart
7	chr4:143302200-143323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:143308200-143323200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:143309000-143323200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:143309000-143323400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:143313000-143326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:143313400-143322800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:143316000-143323200	Weak transcription	Small Intestine	intestine
14	chr4:143316400-143323400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:143317200-143322400	Weak transcription	NHDF-Ad	bronchial
16	chr4:143318000-143322800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:143318000-143323200	Weak transcription	NHLF	lung
18	chr4:143318000-143324000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:143318600-143321600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:143318600-143322200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:143318600-143322800	Weak transcription	Osteobl	bone
22	chr4:143318600-143323200	Weak transcription	NH-A	brain
23	chr4:143318800-143323200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:143319800-143321800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:143319800-143322000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:143320000-143322200	Genic enhancers	NHEK	skin
27	chr4:143320600-143321800	Enhancers	Primary T cells from cord blood	blood
28	chr4:143320600-143322200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr4:143320600-143322800	Strong transcription	HSMM	muscle
30	chr4:143320600-143324600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr4:143320600-143326600	Active TSS	Primary T cells fromperipheralblood	blood
32	chr4:143320800-143321600	Genic enhancers	Dnd41	blood
33	chr4:143320800-143321800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:143320800-143321800	Genic enhancers	HMEC	breast
35	chr4:143320800-143322000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr4:143320800-143322000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:143320800-143323600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr4:143320800-143328000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:143321000-143321600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:143321000-143321800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:143321000-143321800	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr4:143321000-143326800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:143321200-143322000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:143321200-143323200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:143321200-143323200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:143321200-143323400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:143321200-143323400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:143321400-143321600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr4:143321400-143321800	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr4:143321400-143321800	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links