Variant report

Variant	rs2081853
Chromosome Location	chr5:79964349-79964350
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:79949741..79953345-chr5:79963177..79965614,3	K562	blood:
2	chr5:79948482..79951173-chr5:79961260..79964699,4	MCF-7	breast:
3	chr5:79784119..79786030-chr5:79964336..79965848,2	MCF-7	breast:
4	chr5:79864951..79867602-chr5:79962481..79965182,3	MCF-7	breast:
5	chr5:79956607..79959193-chr5:79962502..79964568,2	MCF-7	breast:
6	chr5:79963791..79966264-chr5:79966320..79968324,2	MCF-7	breast:
7	chr5:79959827..79961745-chr5:79962101..79964799,2	K562	blood:
8	chr5:79964150..79966462-chr5:79974912..79977180,3	MCF-7	breast:
9	chr5:79949216..79952432-chr5:79962559..79966205,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000113318	Chromatin interaction
ENSG00000189127	Chromatin interaction
ENSG00000228716	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs408626	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151603	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151617	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6864512	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6868774	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883090	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6887400	0.82[EUR][1000 genomes]
rs7712332	0.82[EUR][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	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
2	nsv10710	chr5:79956446-79964949	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2081853	DHFR	cis	Muscle Skeletal	GTEx
rs2081853	DHFR	cis	Esophagus Muscularis	GTEx
rs2081853	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs2081853	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951600-79969200	Weak transcription	Stomach Mucosa	stomach
2	chr5:79951600-79972200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
4	chr5:79951800-79982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:79952200-79975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:79952400-79965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:79952400-79967400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:79952400-79975400	Weak transcription	HSMMtube	muscle
9	chr5:79952400-79976600	Strong transcription	Fetal Thymus	thymus
10	chr5:79952400-79976800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr5:79952400-79983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:79952600-79965000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:79952600-79985200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:79952600-79991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:79952800-79972200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:79953000-79966400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:79953200-79965200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:79953200-79980800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:79953800-79969800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:79955200-79964400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr5:79955400-79968800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:79955800-79964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:79956200-79979000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
25	chr5:79957600-79964400	Strong transcription	Fetal Lung	lung
26	chr5:79957600-79964600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:79957800-79964800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:79958200-79968800	Weak transcription	Brain Anterior Caudate	brain
29	chr5:79958200-79971600	Strong transcription	Fetal Muscle Leg	muscle
30	chr5:79958200-79998000	Weak transcription	Fetal Brain Male	brain
31	chr5:79958800-79969800	Strong transcription	Primary T cells from cord blood	blood
32	chr5:79959200-79964800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr5:79959400-79965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:79959800-79964600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:79961000-79964800	Strong transcription	Ovary	ovary
36	chr5:79961000-79970200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:79961200-79964400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:79961200-79964400	Strong transcription	Colonic Mucosa	Colon
39	chr5:79961200-79966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:79961200-79977000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:79961400-79965000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:79961400-79967200	Weak transcription	K562	blood
43	chr5:79961400-79968400	Weak transcription	HUVEC	blood vessel
44	chr5:79961400-79968400	Weak transcription	NHDF-Ad	bronchial
45	chr5:79961600-79965600	Weak transcription	Hela-S3	cervix
46	chr5:79961600-79974000	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:79962000-79969800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:79962400-79964800	Genic enhancers	Adipose Nuclei	Adipose
49	chr5:79962400-79964800	Strong transcription	Gastric	stomach
50	chr5:79962400-79964800	Strong transcription	Lung	lung

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