Variant report

Variant	rs6884828
Chromosome Location	chr5:114564946-114564947
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10045548	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10059069	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10079380	0.88[ASN][1000 genomes]
rs11745083	0.80[ASN][1000 genomes]
rs11745170	0.80[ASN][1000 genomes]
rs11960213	0.83[ASN][1000 genomes]
rs17640052	0.81[EUR][1000 genomes]
rs2303001	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs265417	0.88[ASN][1000 genomes]
rs265437	0.91[ASN][1000 genomes]
rs3805580	0.81[EUR][1000 genomes]
rs3805581	0.81[EUR][1000 genomes]
rs3805586	0.89[ASN][1000 genomes]
rs62383165	0.93[ASN][1000 genomes]
rs67276221	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6878733	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7706217	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7725831	0.80[EUR][1000 genomes]
rs9326954	0.83[EUR][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	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1029371	chr5:114541428-114590891	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6884828	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs6884828	PGGT1B	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
2	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
3	chr5:114530800-114565200	Weak transcription	NHDF-Ad	bronchial
4	chr5:114538400-114567000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:114538400-114572000	Weak transcription	Lung	lung
6	chr5:114539200-114580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:114539800-114566000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:114540800-114567600	Weak transcription	Hela-S3	cervix
9	chr5:114541800-114573400	Weak transcription	NHLF	lung
10	chr5:114542000-114575800	Weak transcription	Small Intestine	intestine
11	chr5:114543800-114565400	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:114543800-114577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:114546800-114575600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:114546800-114578000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:114547600-114577600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr5:114547800-114578400	Weak transcription	Esophagus	oesophagus
17	chr5:114547800-114596600	Weak transcription	Brain Germinal Matrix	brain
18	chr5:114548400-114596800	Weak transcription	K562	blood
19	chr5:114548800-114575400	Weak transcription	Brain Substantia Nigra	brain
20	chr5:114549400-114597200	Weak transcription	Aorta	Aorta
21	chr5:114549600-114565400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:114549600-114565600	Weak transcription	Osteobl	bone
23	chr5:114549600-114574400	Weak transcription	HMEC	breast
24	chr5:114550200-114568400	Weak transcription	NHEK	skin
25	chr5:114550200-114575400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr5:114550400-114572600	Weak transcription	A549	lung
27	chr5:114552200-114574600	Weak transcription	Fetal Stomach	stomach
28	chr5:114552200-114581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:114554200-114574600	Weak transcription	Right Ventricle	heart
30	chr5:114554600-114573000	Weak transcription	Brain Angular Gyrus	brain
31	chr5:114554800-114568200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr5:114555800-114579800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr5:114556000-114568000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:114556200-114578000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:114556400-114575600	Weak transcription	Fetal Brain Male	brain
36	chr5:114557000-114577400	Weak transcription	Fetal Heart	heart
37	chr5:114557800-114579400	Weak transcription	Gastric	stomach
38	chr5:114558000-114579400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:114558800-114568000	Strong transcription	Dnd41	blood
40	chr5:114559000-114565200	Weak transcription	Fetal Brain Female	brain
41	chr5:114559000-114587600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:114559400-114578200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:114559400-114579400	Weak transcription	Spleen	Spleen
44	chr5:114560200-114568000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:114560600-114567600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:114560600-114577400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr5:114561400-114566000	Strong transcription	Fetal Muscle Leg	muscle
48	chr5:114561600-114567600	Strong transcription	Placenta	Placenta
49	chr5:114561600-114568000	Strong transcription	Liver	Liver
50	chr5:114561600-114568600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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