Variant report

Variant	rs11950355
Chromosome Location	chr5:114605934-114605935
allele	A/C
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: 6 )

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

rs_ID	r²[population]
rs10059320	0.91[JPT][hapmap]
rs10077453	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1017208	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17459144	0.84[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305130	1.00[JPT][hapmap]
rs28379874	0.96[ASN][1000 genomes]
rs2909842	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909843	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925185	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925186	0.92[CEU][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2963769	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2963770	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963771	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2963772	0.92[ASN][1000 genomes]
rs2963773	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2963774	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2964543	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2964544	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35948019	0.96[ASN][1000 genomes]
rs4041	1.00[JPT][hapmap]
rs4705732	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7734074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11950355	PGGT1B	cis	uninvolved skin	skin_eQTL
rs11950355	PGGT1B	cis	multi-tissue	Pritchard
rs11950355	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs11950355	PGGT1B	cis	lymphoblastoid	seeQTL
rs11950355	CCDC112	cis	parietal	SCAN
rs11950355	PGGT1B	cis	lesional skin	skin_eQTL

Chromatin state (count:101 , 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	chr5:114599000-114606200	Weak transcription	HSMMtube	muscle
5	chr5:114599000-114606400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:114599000-114606400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:114599000-114608800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:114599000-114610200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:114599000-114610200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:114599000-114610400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:114599000-114610600	Weak transcription	Pancreas	Pancrea
12	chr5:114599000-114610600	Weak transcription	NHLF	lung
13	chr5:114599000-114612200	Weak transcription	Right Ventricle	heart
14	chr5:114599000-114612800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr5:114599000-114612800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:114599000-114612800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:114599000-114612800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:114599000-114612800	Weak transcription	Fetal Intestine Large	intestine
19	chr5:114599000-114612800	Weak transcription	Fetal Thymus	thymus
20	chr5:114599000-114614200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:114599000-114617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:114599000-114617200	Weak transcription	Thymus	Thymus
23	chr5:114599000-114624000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:114599000-114626600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:114599000-114630800	Weak transcription	Psoas Muscle	Psoas
26	chr5:114599000-114631200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:114599000-114631200	Weak transcription	HSMM	muscle
28	chr5:114599000-114631400	Weak transcription	Left Ventricle	heart
29	chr5:114599200-114606200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:114599200-114606200	Weak transcription	Primary T cells from cord blood	blood
31	chr5:114599200-114606200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:114599200-114606200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:114599200-114606400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr5:114599200-114606400	Weak transcription	Primary B cells from cord blood	blood
35	chr5:114599200-114606400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr5:114599200-114606400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:114599200-114608000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:114599200-114608000	Weak transcription	Adipose Nuclei	Adipose
39	chr5:114599200-114608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:114599200-114608800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:114599200-114609200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:114599200-114609200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:114599200-114609400	Weak transcription	Colonic Mucosa	Colon
44	chr5:114599200-114610200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:114599200-114610400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:114599200-114610400	Weak transcription	Fetal Lung	lung
47	chr5:114599200-114610400	Weak transcription	A549	lung
48	chr5:114599200-114611000	Weak transcription	Ovary	ovary
49	chr5:114599200-114611800	Weak transcription	Fetal Kidney	kidney
50	chr5:114599200-114612000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links