Variant report

Variant	rs6883090
Chromosome Location	chr5:79976388-79976389
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79964150..79966462-chr5:79974912..79977180,3	MCF-7	breast:
2	chr5:79970108..79972408-chr5:79975282..79977185,2	MCF-7	breast:
3	chr5:79782620..79784555-chr5:79974141..79977090,2	MCF-7	breast:
4	chr5:79782909..79785526-chr5:79974882..79977098,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152380	Chromatin interaction
ENSG00000249042	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10036806	0.83[ASN][1000 genomes]
rs10044991	0.83[ASN][1000 genomes]
rs1621852	0.87[ASN][1000 genomes]
rs1650649	0.85[ASN][1000 genomes]
rs1650748	0.87[ASN][1000 genomes]
rs1650751	0.87[ASN][1000 genomes]
rs1677646	0.82[ASN][1000 genomes]
rs2081853	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3776964	0.81[ASN][1000 genomes]
rs6151603	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151617	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6864512	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868774	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836805	0.87[ASN][1000 genomes]

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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6883090	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs6883090	DHFR	cis	Muscle Skeletal	GTEx
rs6883090	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs6883090	DHFR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
2	chr5:79951800-79982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:79952400-79976600	Strong transcription	Fetal Thymus	thymus
4	chr5:79952400-79976800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr5:79952400-79983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:79952600-79985200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:79952600-79991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:79953200-79980800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr5:79956200-79979000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
11	chr5:79958200-79998000	Weak transcription	Fetal Brain Male	brain
12	chr5:79961200-79977000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:79962800-80015600	Weak transcription	A549	lung
14	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
15	chr5:79963800-79979600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:79964000-79977800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:79964000-79984600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:79964000-79984800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:79964000-79998000	Weak transcription	Aorta	Aorta
20	chr5:79964400-79977800	Weak transcription	Esophagus	oesophagus
21	chr5:79964400-79983200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:79964400-79999200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:79964600-79983000	Weak transcription	Brain Angular Gyrus	brain
24	chr5:79964800-79976800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr5:79964800-79998000	Weak transcription	Gastric	stomach
26	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:79965000-79977200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr5:79965000-80021400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:79965200-79980400	Weak transcription	Brain Germinal Matrix	brain
30	chr5:79965600-79978400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:79965800-79978400	Strong transcription	Dnd41	blood
32	chr5:79966000-79976600	Strong transcription	Fetal Intestine Large	intestine
33	chr5:79967000-79977000	Strong transcription	Primary hematopoietic stem cells	blood
34	chr5:79968200-79979200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:79968400-79976600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:79968600-79976600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:79968600-79976800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:79969400-79979000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:79969400-80001200	Weak transcription	NHLF	lung
40	chr5:79969600-80010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:79969800-79997000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:79970400-79997000	Weak transcription	K562	blood
43	chr5:79971600-79978400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:79971600-79989800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:79971600-79999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:79971600-80022200	Weak transcription	HMEC	breast
47	chr5:79971800-79978000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:79971800-79999200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:79971800-80003400	Weak transcription	NHDF-Ad	bronchial
50	chr5:79971800-80015400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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