Variant report

Variant	rs28379874
Chromosome Location	chr5:114606553-114606554
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	chr5:114593990..114598856-chr5:114605325..114609897,4	K562	blood:
2	chr5:114604992..114607279-chr5:114608141..114610271,2	K562	blood:

Variant related genes	Relation type
ENSG00000164219	Chromatin interaction
ENSG00000271797	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10077453	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1017208	0.96[ASN][1000 genomes]
rs11950355	0.96[ASN][1000 genomes]
rs13152930	0.80[EUR][1000 genomes]
rs13172537	0.81[EUR][1000 genomes]
rs17459144	0.89[ASN][1000 genomes]
rs2909842	0.93[ASN][1000 genomes]
rs2909843	0.92[ASN][1000 genomes]
rs2925185	0.96[ASN][1000 genomes]
rs2963769	0.89[ASN][1000 genomes]
rs2963770	0.92[ASN][1000 genomes]
rs2963771	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963772	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963773	0.85[ASN][1000 genomes]
rs2963774	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2964543	0.89[ASN][1000 genomes]
rs2964544	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34434304	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35948019	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705732	0.89[ASN][1000 genomes]
rs7734074	0.96[ASN][1000 genomes]
rs9326953	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326956	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28379874	PGGT1B	cis	multi-tissue	Pritchard
rs28379874	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114598800-114608200	Weak transcription	Small Intestine	intestine
2	chr5:114598800-114612200	Weak transcription	Gastric	stomach
3	chr5:114598800-114613000	Weak transcription	Esophagus	oesophagus
4	chr5:114599000-114608800	Weak transcription	Brain Substantia Nigra	brain
5	chr5:114599000-114610200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:114599000-114610200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:114599000-114610400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:114599000-114610600	Weak transcription	Pancreas	Pancrea
9	chr5:114599000-114610600	Weak transcription	NHLF	lung
10	chr5:114599000-114612200	Weak transcription	Right Ventricle	heart
11	chr5:114599000-114612800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:114599000-114612800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:114599000-114612800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:114599000-114612800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:114599000-114612800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:114599000-114612800	Weak transcription	Fetal Thymus	thymus
17	chr5:114599000-114614200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:114599000-114617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:114599000-114617200	Weak transcription	Thymus	Thymus
20	chr5:114599000-114624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:114599000-114626600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:114599000-114630800	Weak transcription	Psoas Muscle	Psoas
23	chr5:114599000-114631200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:114599000-114631200	Weak transcription	HSMM	muscle
25	chr5:114599000-114631400	Weak transcription	Left Ventricle	heart
26	chr5:114599200-114608000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:114599200-114608000	Weak transcription	Adipose Nuclei	Adipose
28	chr5:114599200-114608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:114599200-114608800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr5:114599200-114609200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:114599200-114609200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:114599200-114609400	Weak transcription	Colonic Mucosa	Colon
33	chr5:114599200-114610200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:114599200-114610400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:114599200-114610400	Weak transcription	Fetal Lung	lung
36	chr5:114599200-114610400	Weak transcription	A549	lung
37	chr5:114599200-114611000	Weak transcription	Ovary	ovary
38	chr5:114599200-114611800	Weak transcription	Fetal Kidney	kidney
39	chr5:114599200-114612000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:114599200-114612600	Weak transcription	NH-A	brain
41	chr5:114599200-114612800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:114599200-114615000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:114599200-114615000	Weak transcription	Fetal Brain Male	brain
44	chr5:114599200-114616400	Weak transcription	Fetal Heart	heart
45	chr5:114599200-114622000	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:114599200-114631200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:114599400-114608800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:114599400-114610600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:114599400-114612200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr5:114599400-114613400	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links