Variant report

Variant	rs8052900
Chromosome Location	chr16:11940390-11940391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:11936442..11940721-chr16:11941344..11946764,13	K562	blood:
2	chr16:11940299..11942446-chr16:11943353..11945680,3	K562	blood:
3	chr16:11918375..11921492-chr16:11938739..11940419,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263307	Chromatin interaction
ENSG00000171490	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10852340	0.85[ASN][1000 genomes]
rs190461	0.81[EUR][1000 genomes]
rs2018199	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075158	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2098722	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33621	0.81[EUR][1000 genomes]
rs33624	0.81[EUR][1000 genomes]
rs33629	0.84[EUR][1000 genomes]
rs33630	0.81[EUR][1000 genomes]
rs33635	0.86[EUR][1000 genomes]
rs33648	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33654	0.90[EUR][1000 genomes]
rs3971913	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs42424	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4429311	0.85[ASN][1000 genomes]
rs4493057	0.86[ASN][1000 genomes]
rs4561483	0.87[ASN][1000 genomes]
rs6498250	0.87[ASN][1000 genomes]
rs7202234	0.83[EUR][1000 genomes]
rs9927765	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482288	chr16:11776491-11946429	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8052900	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11918600-11943800	Weak transcription	Right Atrium	heart
2	chr16:11928400-11942000	Strong transcription	Primary T cells from cord blood	blood
3	chr16:11929200-11943000	Strong transcription	Lung	lung
4	chr16:11929200-11944000	Strong transcription	Fetal Stomach	stomach
5	chr16:11929400-11942200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr16:11929400-11942800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:11929400-11942800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr16:11929400-11943000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:11929400-11943000	Strong transcription	Fetal Intestine Small	intestine
10	chr16:11929400-11943200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr16:11929400-11943400	Strong transcription	Brain Germinal Matrix	brain
12	chr16:11929400-11943600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr16:11929400-11943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr16:11929600-11940800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr16:11929600-11941000	Strong transcription	Brain Hippocampus Middle	brain
16	chr16:11929600-11942600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:11929600-11942600	Strong transcription	Thymus	Thymus
18	chr16:11929600-11943000	Strong transcription	Rectal Smooth Muscle	rectum
19	chr16:11929600-11943200	Strong transcription	Brain Anterior Caudate	brain
20	chr16:11929600-11943200	Strong transcription	Fetal Brain Female	brain
21	chr16:11929600-11943200	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr16:11929600-11944000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr16:11929800-11942000	Strong transcription	Pancreas	Pancrea
24	chr16:11929800-11942400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr16:11929800-11943200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr16:11929800-11943400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr16:11929800-11943400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr16:11930000-11941000	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr16:11930000-11941400	Strong transcription	Ovary	ovary
30	chr16:11930000-11941600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr16:11930000-11941800	Strong transcription	Dnd41	blood
32	chr16:11930000-11942400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr16:11930000-11942400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr16:11930000-11942600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr16:11930000-11942800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr16:11930000-11942800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:11930000-11943000	Strong transcription	Brain Cingulate Gyrus	brain
38	chr16:11930000-11943000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr16:11930000-11943200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr16:11930000-11943200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr16:11930000-11943400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr16:11930000-11943400	Strong transcription	Brain Angular Gyrus	brain
43	chr16:11930000-11943400	Strong transcription	Fetal Intestine Large	intestine
44	chr16:11930000-11943600	Strong transcription	Fetal Muscle Leg	muscle
45	chr16:11930000-11943800	Strong transcription	Liver	Liver
46	chr16:11930000-11944000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr16:11930000-11944000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:11930200-11940600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr16:11930200-11941600	Strong transcription	GM12878-XiMat	blood
50	chr16:11930200-11941600	Strong transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links