Variant report

Variant	rs245351
Chromosome Location	chr5:80153541-80153542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1644201	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs245338	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245343	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245345	0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245346	0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245362	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245378	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245392	0.82[JPT][hapmap]
rs32982	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs32991	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32993	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33002	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4704688	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6870725	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs245351	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs245351	DHFR	cis	Muscle Skeletal	GTEx
rs245351	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs245351	DHFR	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
2	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
4	chr5:80125200-80161600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:80141200-80161000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:80141200-80178800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:80143000-80175400	Weak transcription	HMEC	breast
8	chr5:80143800-80156600	Weak transcription	Osteobl	bone
9	chr5:80145600-80153800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:80145600-80157000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:80145600-80172800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:80145600-80175600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:80145600-80181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:80145800-80167400	Weak transcription	Placenta	Placenta
15	chr5:80145800-80173400	Weak transcription	Colonic Mucosa	Colon
16	chr5:80146000-80173400	Weak transcription	Esophagus	oesophagus
17	chr5:80146400-80162600	Weak transcription	Fetal Stomach	stomach
18	chr5:80146400-80162800	Weak transcription	Gastric	stomach
19	chr5:80146400-80167200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:80146400-80167200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:80146400-80170600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:80146400-80173400	Weak transcription	Brain Substantia Nigra	brain
23	chr5:80146600-80162000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:80146800-80161600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:80146800-80161800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:80148400-80167400	Weak transcription	HSMM	muscle
27	chr5:80148600-80175600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:80148800-80156800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:80148800-80173200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:80149000-80161800	Weak transcription	HepG2	liver
31	chr5:80149200-80153800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:80149200-80157000	Weak transcription	HSMMtube	muscle
33	chr5:80149200-80166000	Weak transcription	K562	blood
34	chr5:80149200-80167200	Weak transcription	Hela-S3	cervix
35	chr5:80149200-80176200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:80149800-80180000	Weak transcription	Psoas Muscle	Psoas
37	chr5:80150600-80154200	Strong transcription	Primary T cells from cord blood	blood
38	chr5:80150800-80156600	Weak transcription	Fetal Heart	heart
39	chr5:80151000-80153600	ZNF genes & repeats	GM12878-XiMat	blood
40	chr5:80151200-80173000	Weak transcription	Fetal Brain Male	brain
41	chr5:80151400-80153600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
42	chr5:80151400-80161800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:80151600-80162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:80151600-80175600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:80151800-80153800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:80151800-80153800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
47	chr5:80151800-80162600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:80152000-80154000	Weak transcription	Fetal Intestine Small	intestine
49	chr5:80152000-80157000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:80152000-80157000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links