Variant report

Variant	rs997421
Chromosome Location	chr5:58429642-58429643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10062340	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10062397	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1038080	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12654485	0.88[CEU][hapmap]
rs13176291	0.90[CHB][hapmap]
rs13176475	0.90[CHB][hapmap]
rs1551939	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16877156	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2409628	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs33927508	0.88[CEU][hapmap]
rs35728243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700321	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6450507	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7707392	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7707566	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7730574	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9292195	0.83[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58424000-58439800	Weak transcription	Small Intestine	intestine
2	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58424200-58432800	Weak transcription	Right Ventricle	heart
4	chr5:58424200-58446200	Weak transcription	Fetal Intestine Large	intestine
5	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58424400-58430200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:58424400-58431400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:58425800-58429800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:58426600-58430200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:58426800-58430200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:58426800-58431200	Enhancers	Primary T cells from cord blood	blood
12	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:58427400-58430000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:58428000-58431000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr5:58428800-58430200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:58428800-58435800	Weak transcription	Fetal Heart	heart
17	chr5:58429000-58430800	Enhancers	NHDF-Ad	bronchial
18	chr5:58429200-58431200	Enhancers	Hela-S3	cervix
19	chr5:58429400-58429800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:58429400-58429800	Enhancers	Left Ventricle	heart
21	chr5:58429400-58429800	Enhancers	Right Atrium	heart
22	chr5:58429400-58430000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:58429400-58430000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:58429400-58430000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:58429400-58430000	Enhancers	Aorta	Aorta
26	chr5:58429400-58430000	Enhancers	Colon Smooth Muscle	Colon
27	chr5:58429400-58430000	Enhancers	Psoas Muscle	Psoas
28	chr5:58429400-58430000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr5:58429400-58430000	Enhancers	HMEC	breast
30	chr5:58429400-58430200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:58429400-58430400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:58429400-58430600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:58429400-58430600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:58429400-58431200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:58429400-58431200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:58429600-58429800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:58429600-58430000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:58429600-58430000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:58429600-58430000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr5:58429600-58430200	Genic enhancers	A549	lung
41	chr5:58429600-58430800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:58429600-58430800	Enhancers	Osteobl	bone
43	chr5:58429600-58431000	Enhancers	HSMM	muscle

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