Variant report

Variant	rs62368679
Chromosome Location	chr5:80888773-80888774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514230	0.89[ASN][1000 genomes]
rs10942274	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10942275	0.85[ASN][1000 genomes]
rs11738820	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11743304	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11745832	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11749863	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12517941	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521077	0.82[ASN][1000 genomes]
rs12521151	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13157978	0.87[ASN][1000 genomes]
rs13158214	0.90[ASN][1000 genomes]
rs13170372	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13171787	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13173845	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13184174	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13436668	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1971177	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2060584	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34307657	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34365981	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35340025	0.90[EUR][1000 genomes]
rs35862056	0.90[ASN][1000 genomes]
rs62366251	0.84[EUR][1000 genomes]
rs62366269	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62368677	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71636282	0.85[ASN][1000 genomes]
rs72773052	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7707981	0.90[ASN][1000 genomes]
rs7711576	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7720445	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7726379	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][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	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv525437	chr5:80876359-80964452	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80864200-80894200	Weak transcription	Fetal Lung	lung
2	chr5:80864600-80894200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:80870800-80894200	Weak transcription	Primary B cells from cord blood	blood
4	chr5:80875600-80894000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:80875600-80894200	Weak transcription	GM12878-XiMat	blood
6	chr5:80876000-80894200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:80881400-80894200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:80883200-80905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr5:80883800-80909200	Weak transcription	HSMM	muscle
10	chr5:80885000-80894200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:80885200-80905400	Weak transcription	Pancreas	Pancrea
12	chr5:80886400-80888800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:80886800-80905400	Weak transcription	Brain Substantia Nigra	brain
14	chr5:80887000-80894400	Weak transcription	Left Ventricle	heart
15	chr5:80887000-80905600	Weak transcription	Brain Anterior Caudate	brain
16	chr5:80887000-80922400	Weak transcription	Psoas Muscle	Psoas
17	chr5:80887200-80894200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:80887200-80894200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:80887200-80894400	Weak transcription	Primary T cells from cord blood	blood
20	chr5:80887200-80894400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:80887200-80894400	Weak transcription	Thymus	Thymus
22	chr5:80887200-80898000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:80887200-80905400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:80887200-80911200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr5:80887400-80904600	Weak transcription	Osteobl	bone
26	chr5:80887600-80888800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr5:80887600-80888800	ZNF genes & repeats	Fetal Stomach	stomach
28	chr5:80887600-80888800	ZNF genes & repeats	Fetal Thymus	thymus
29	chr5:80887800-80889800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:80887800-80892800	Weak transcription	Dnd41	blood
31	chr5:80888400-80888800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
32	chr5:80888400-80888800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
33	chr5:80888400-80888800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:80888600-80894000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:80888600-80894000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:80888600-80905200	Weak transcription	Brain Germinal Matrix	brain
37	chr5:80888600-80905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links