Variant report

Variant	rs57527145
Chromosome Location	chr5:58304045-58304046
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58187276..58188206-chr5:58302963..58304103,9	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10036287	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10053177	0.82[AFR][1000 genomes]
rs10053330	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10061320	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10063703	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10065498	0.80[ASN][1000 genomes]
rs10065540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10223103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940638	0.82[AFR][1000 genomes]
rs11750426	0.82[AFR][1000 genomes]
rs11957827	0.82[AFR][1000 genomes]
rs16888990	0.82[AFR][1000 genomes]
rs16888998	0.82[AFR][1000 genomes]
rs1874857	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1874858	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1874859	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2055296	0.82[AFR][1000 genomes]
rs2055297	0.82[AFR][1000 genomes]
rs2055298	0.82[AFR][1000 genomes]
rs4469166	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4493634	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4631140	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4699932	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4700315	0.82[AFR][1000 genomes]
rs4700316	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700317	0.82[AFR][1000 genomes]
rs58940834	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61511922	0.81[ASN][1000 genomes]
rs62358490	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs62358491	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62358492	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6450498	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6876057	0.82[AFR][1000 genomes]
rs7723432	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727206	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283720	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9292188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292189	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv526881	chr5:58302980-58304499	Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58279200-58314000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:58279400-58317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:58279600-58330400	Weak transcription	Fetal Stomach	stomach
4	chr5:58281800-58321600	Weak transcription	Osteobl	bone
5	chr5:58282400-58306600	Weak transcription	Fetal Intestine Small	intestine
6	chr5:58286200-58312800	Weak transcription	Lung	lung
7	chr5:58286200-58316200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:58286200-58330400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:58286200-58330600	Weak transcription	Thymus	Thymus
10	chr5:58286800-58312200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:58286800-58312600	Weak transcription	Fetal Thymus	thymus
12	chr5:58286800-58312800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:58288800-58330600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:58293400-58305200	Enhancers	Primary T cells from cord blood	blood
15	chr5:58296000-58312400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:58296000-58321600	Weak transcription	Aorta	Aorta
17	chr5:58298400-58312600	Weak transcription	Fetal Lung	lung
18	chr5:58298600-58317800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:58299600-58312400	Weak transcription	HSMM	muscle
20	chr5:58299600-58316600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:58299800-58306600	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:58299800-58318000	Weak transcription	Right Ventricle	heart
23	chr5:58301200-58313000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:58301400-58304200	Enhancers	Hela-S3	cervix
25	chr5:58301400-58305000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:58302000-58312800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:58302000-58315200	Weak transcription	Psoas Muscle	Psoas
28	chr5:58302200-58304400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:58302200-58305800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:58302200-58306400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr5:58302400-58312200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:58302400-58312800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:58302400-58316200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:58302400-58321600	Weak transcription	Gastric	stomach
35	chr5:58302800-58304800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:58302800-58312600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:58302800-58312800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:58302800-58315200	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:58303000-58305000	Flanking Active TSS	A549	lung
40	chr5:58303200-58305000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr5:58303200-58305200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:58303400-58306400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:58303600-58317800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:58303800-58304200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr5:58303800-58305000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr5:58303800-58306800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:58304000-58316800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:58304000-58316800	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links