Variant report

Variant	rs6864493
Chromosome Location	chr5:79985702-79985703
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	chr5:79984859..79986713-chr5:79993487..79995213,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17205503	0.95[EUR][1000 genomes]
rs245392	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs28059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs33008	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap]
rs6151604	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151629	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6861850	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6887400	0.85[ASN][1000 genomes]
rs73129108	0.88[AFR][1000 genomes]
rs73132417	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7712332	0.81[CHB][hapmap];0.85[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6864493	DHFR	cis	Muscle Skeletal	GTEx

Chromatin state (count:105 , 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	chr5:79952600-79991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
4	chr5:79958200-79998000	Weak transcription	Fetal Brain Male	brain
5	chr5:79962800-80015600	Weak transcription	A549	lung
6	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
7	chr5:79964000-79998000	Weak transcription	Aorta	Aorta
8	chr5:79964400-79999200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:79964800-79998000	Weak transcription	Gastric	stomach
10	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:79965000-80021400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:79969400-80001200	Weak transcription	NHLF	lung
13	chr5:79969600-80010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:79969800-79997000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:79970400-79997000	Weak transcription	K562	blood
16	chr5:79971600-79989800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:79971600-79999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:79971600-80022200	Weak transcription	HMEC	breast
19	chr5:79971800-79999200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:79971800-80003400	Weak transcription	NHDF-Ad	bronchial
21	chr5:79971800-80015400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:79972400-79999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:79972400-80010400	Weak transcription	NHEK	skin
25	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:79972800-80001600	Weak transcription	HUVEC	blood vessel
27	chr5:79973200-80021600	Weak transcription	NH-A	brain
28	chr5:79973400-80008800	Weak transcription	Brain Anterior Caudate	brain
29	chr5:79974000-80003000	Weak transcription	Fetal Heart	heart
30	chr5:79974000-80021200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:79975000-79998000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:79975200-80022800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:79975600-80015200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:79975600-80022000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:79975800-79992000	Weak transcription	Fetal Lung	lung
36	chr5:79975800-79997000	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:79975800-80002800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:79975800-80004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:79975800-80007000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:79975800-80008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:79975800-80009200	Weak transcription	Pancreas	Pancrea
42	chr5:79975800-80015600	Weak transcription	Brain Substantia Nigra	brain
43	chr5:79975800-80015800	Weak transcription	Fetal Brain Female	brain
44	chr5:79976000-79985800	Weak transcription	Fetal Intestine Small	intestine
45	chr5:79976000-79991800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:79976000-79991800	Weak transcription	Lung	lung
47	chr5:79976000-79998000	Weak transcription	Ovary	ovary
48	chr5:79976000-79999200	Weak transcription	Osteobl	bone
49	chr5:79976000-80000000	Weak transcription	Thymus	Thymus
50	chr5:79976000-80010400	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links