Variant report

Variant	rs28059
Chromosome Location	chr5:80038965-80038966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80037673..80040180-chr5:80041724..80043990,2	K562	blood:

Variant related genes	Relation type
ENSG00000248967	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs151886	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245009	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245014	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245336	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245392	0.92[CEU][hapmap];0.87[YRI][hapmap]
rs245398	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245404	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26781	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32951	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32953	0.93[EUR][1000 genomes]
rs32960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33008	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33011	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776972	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40592	0.81[EUR][1000 genomes]
rs41097	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6151629	0.95[CEU][hapmap];0.93[YRI][hapmap]
rs6151653	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6151670	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap]
rs6151706	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151707	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7712332	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv2452635	chr5:80038541-80040159	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3421113	chr5:80038646-80040644	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28059	DHFR	cis	Muscle Skeletal	GTEx
rs28059	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
4	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
5	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
7	chr5:80009800-80039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:80016000-80040600	Weak transcription	Small Intestine	intestine
9	chr5:80016200-80040600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:80016200-80040600	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
13	chr5:80020200-80043600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:80022200-80040000	Weak transcription	K562	blood
15	chr5:80022800-80040600	Weak transcription	Spleen	Spleen
16	chr5:80022800-80041400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:80022800-80051200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:80023000-80040600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr5:80023000-80040600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:80023000-80040600	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:80023000-80040600	Weak transcription	HUVEC	blood vessel
22	chr5:80023000-80041400	Weak transcription	Fetal Brain Female	brain
23	chr5:80023000-80043000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:80023000-80043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:80024000-80041400	Weak transcription	NH-A	brain
26	chr5:80024200-80040600	Weak transcription	Brain Anterior Caudate	brain
27	chr5:80024200-80040600	Weak transcription	Brain Substantia Nigra	brain
28	chr5:80024200-80046800	Weak transcription	Brain Angular Gyrus	brain
29	chr5:80024400-80043400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:80024600-80039000	Weak transcription	Fetal Lung	lung
31	chr5:80025800-80039000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:80026000-80039800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:80026000-80042000	Weak transcription	GM12878-XiMat	blood
34	chr5:80026200-80040600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:80026400-80040000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:80032400-80045400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr5:80032800-80043600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:80033200-80051400	Weak transcription	HMEC	breast
39	chr5:80034200-80049400	Strong transcription	Primary T cells from cord blood	blood
40	chr5:80034800-80050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr5:80035000-80050400	Weak transcription	Stomach Mucosa	stomach
42	chr5:80035200-80042200	Weak transcription	HSMMtube	muscle
43	chr5:80036200-80041400	Weak transcription	NHLF	lung
44	chr5:80036400-80039400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:80036400-80043800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr5:80036800-80039000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:80037000-80039000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:80037000-80042400	Strong transcription	Fetal Thymus	thymus
49	chr5:80037200-80039000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:80037200-80040800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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