Variant report

Variant	rs42290
Chromosome Location	chr5:80089022-80089023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80087165..80090080-chr5:80096235..80098105,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1650723	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1650734	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1650735	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1650736	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs245361	0.83[AFR][1000 genomes]
rs245387	0.81[EUR][1000 genomes]
rs245394	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs245395	0.80[AMR][1000 genomes]
rs245396	0.80[AMR][1000 genomes]
rs245397	0.84[AMR][1000 genomes]
rs245399	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs245400	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs245403	0.96[EUR][1000 genomes]
rs245408	0.94[EUR][1000 genomes]
rs26266	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs26268	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs26283	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs27365	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28026	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs32958	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs32994	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs32998	0.86[EUR][1000 genomes]
rs33000	0.86[EUR][1000 genomes]
rs33009	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33010	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs39628	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6151616	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs836790	1.00[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs42290	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:80041200-80100400	Weak transcription	Gastric	stomach
5	chr5:80041800-80094200	Weak transcription	NHLF	lung
6	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
7	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
8	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
9	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
10	chr5:80051600-80095000	Weak transcription	Psoas Muscle	Psoas
11	chr5:80052200-80095600	Weak transcription	Fetal Brain Male	brain
12	chr5:80057200-80090000	Weak transcription	Aorta	Aorta
13	chr5:80057200-80094200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:80057400-80089200	Weak transcription	K562	blood
15	chr5:80059600-80089200	Weak transcription	Lung	lung
16	chr5:80064800-80089200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr5:80069000-80093600	Weak transcription	Pancreas	Pancrea
18	chr5:80069400-80089200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:80073200-80093600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:80073600-80089200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:80073600-80089600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:80074000-80090600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:80075200-80114000	Weak transcription	Stomach Mucosa	stomach
25	chr5:80076200-80109600	Weak transcription	HepG2	liver
26	chr5:80076400-80089200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr5:80076400-80089200	Weak transcription	Ovary	ovary
28	chr5:80076600-80090600	Weak transcription	Small Intestine	intestine
29	chr5:80077400-80089200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:80077400-80108000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:80077600-80089200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:80077600-80112000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:80077800-80089200	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:80079200-80093400	Weak transcription	NH-A	brain
36	chr5:80080000-80089200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:80080000-80090600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:80081200-80089400	Weak transcription	GM12878-XiMat	blood
39	chr5:80083000-80101400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr5:80083200-80091600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:80083200-80093000	Strong transcription	Liver	Liver
42	chr5:80083200-80093600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:80083200-80098400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr5:80083400-80092800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:80083400-80093600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr5:80083800-80098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:80084000-80092200	Weak transcription	NHDF-Ad	bronchial
48	chr5:80084600-80090600	Weak transcription	Fetal Intestine Small	intestine
49	chr5:80084800-80089400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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