Variant report

Variant	rs6151617
Chromosome Location	chr5:79961643-79961644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79949469..79952058-chr5:79960023..79961648,2	MCF-7	breast:
2	chr5:79959827..79961745-chr5:79962101..79964799,2	K562	blood:
3	chr5:79948482..79951173-chr5:79961260..79964699,4	MCF-7	breast:
4	chr5:79959818..79962346-chr5:79962374..79963921,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228716	Chromatin interaction
ENSG00000113318	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12517451	0.83[JPT][hapmap]
rs1650649	0.89[JPT][hapmap]
rs1650658	0.80[YRI][hapmap]
rs1650666	0.80[YRI][hapmap]
rs1650667	0.80[YRI][hapmap]
rs1650670	0.80[YRI][hapmap]
rs1650697	0.83[JPT][hapmap]
rs1677628	0.80[YRI][hapmap]
rs1677629	0.80[YRI][hapmap]
rs1677635	0.81[YRI][hapmap]
rs1824838	0.80[YRI][hapmap]
rs1824839	0.80[YRI][hapmap]
rs2081853	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs372069	0.81[ASN][1000 genomes]
rs380691	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs384925	0.81[ASN][1000 genomes]
rs408626	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs442767	0.83[ASN][1000 genomes]
rs443611	0.81[ASN][1000 genomes]
rs525054	0.80[ASN][1000 genomes]
rs6151603	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151614	0.80[YRI][hapmap]
rs6151620	0.80[YRI][hapmap]
rs6864512	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6868774	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883090	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6887400	0.82[EUR][1000 genomes]
rs7712332	0.82[EUR][1000 genomes]
rs836805	0.87[JPT][hapmap]
rs861365	0.81[ASN][1000 genomes]

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	esv1792078	chr5:79953567-79962367	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv1831340	chr5:79953567-79962367	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv1851181	chr5:79953567-79962367	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv1826846	chr5:79956218-79961861	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1818797	chr5:79956218-79962367	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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
8	esv1851512	chr5:79959188-79962367	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6151617	DHFR	cis	Muscle Skeletal	GTEx
rs6151617	MSH3,DHFR	cis	brain	BrainEAC
rs6151617	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs6151617	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs6151617	DHFR	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951200-79963200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:79951400-79963200	Weak transcription	Right Ventricle	heart
3	chr5:79951600-79962600	Weak transcription	Esophagus	oesophagus
4	chr5:79951600-79963200	Weak transcription	Pancreas	Pancrea
5	chr5:79951600-79963400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:79951600-79963400	Weak transcription	Brain Germinal Matrix	brain
7	chr5:79951600-79963600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:79951600-79969200	Weak transcription	Stomach Mucosa	stomach
9	chr5:79951600-79972200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
11	chr5:79951800-79964000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:79951800-79982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:79952000-79963800	Weak transcription	Fetal Heart	heart
14	chr5:79952200-79964200	Weak transcription	Brain Angular Gyrus	brain
15	chr5:79952200-79964200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr5:79952200-79964200	Weak transcription	NHLF	lung
17	chr5:79952200-79975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:79952400-79963200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:79952400-79963400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:79952400-79965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:79952400-79967400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:79952400-79975400	Weak transcription	HSMMtube	muscle
23	chr5:79952400-79976600	Strong transcription	Fetal Thymus	thymus
24	chr5:79952400-79976800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:79952400-79983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:79952600-79962200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:79952600-79963000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:79952600-79963200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:79952600-79963800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:79952600-79965000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:79952600-79985200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr5:79952600-79991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:79952800-79972200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:79953000-79966400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:79953200-79963400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr5:79953200-79963800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr5:79953200-79964200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:79953200-79964200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:79953200-79965200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:79953200-79980800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr5:79953600-79964200	Strong transcription	Dnd41	blood
42	chr5:79953800-79969800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:79954000-79962000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:79954400-79963400	Weak transcription	NHEK	skin
45	chr5:79954600-79963200	Weak transcription	Spleen	Spleen
46	chr5:79955200-79962400	Weak transcription	Gastric	stomach
47	chr5:79955200-79963200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:79955200-79963200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:79955200-79964400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr5:79955400-79968800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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