Variant report

Variant	rs33649
Chromosome Location	chr16:11979608-11979609
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:11979518-11979690	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000261560	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11075022	0.81[AMR][1000 genomes]
rs11646545	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11647818	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11649405	0.81[AMR][1000 genomes]
rs12925740	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153025	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs154148	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs171656	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075159	0.85[EUR][1000 genomes]
rs251723	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28279	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33619	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33620	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33623	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33629	0.81[EUR][1000 genomes]
rs33631	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33635	0.83[EUR][1000 genomes]
rs33637	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33640	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33643	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33645	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33647	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33648	0.85[EUR][1000 genomes]
rs33651	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33652	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33653	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33654	0.83[EUR][1000 genomes]
rs33655	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33660	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35153773	0.81[AMR][1000 genomes]
rs40311	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42424	0.83[EUR][1000 genomes]
rs4511557	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs718081	0.81[AMR][1000 genomes]
rs7198817	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7202234	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8046617	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8047726	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8061189	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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	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
2	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
3	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
4	nsv984257	chr16:11968206-11992901	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33649	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11961600-11986000	Weak transcription	Stomach Mucosa	stomach
2	chr16:11961800-11991000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:11962000-11992200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr16:11962000-11994600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr16:11962200-11992000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:11962400-11982600	Strong transcription	Fetal Thymus	thymus
7	chr16:11962400-11984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr16:11962400-11990800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr16:11962400-11995000	Strong transcription	Dnd41	blood
14	chr16:11962600-11985600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:11962600-11990600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr16:11962600-11991800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:11964800-11990800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr16:11964800-11991000	Strong transcription	Fetal Intestine Large	intestine
20	chr16:11965000-11986400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr16:11965000-11990200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr16:11965000-11991000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr16:11965200-11991000	Strong transcription	GM12878-XiMat	blood
24	chr16:11965400-11990800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr16:11965400-11991400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr16:11965600-11983000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr16:11965600-11983200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr16:11965600-11991000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr16:11965800-11990200	Strong transcription	Liver	Liver
30	chr16:11965800-11995000	Strong transcription	HepG2	liver
31	chr16:11966000-11982200	Strong transcription	HUVEC	blood vessel
32	chr16:11966000-11991000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:11966000-11991400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:11966200-11984200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr16:11966200-11989400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr16:11966200-12006200	Weak transcription	Fetal Heart	heart
37	chr16:11966600-11979800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr16:11966600-11983800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr16:11966600-11988200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr16:11966600-11991000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr16:11967000-11990200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr16:11969000-11981800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr16:11969000-11984600	Strong transcription	Fetal Muscle Leg	muscle
44	chr16:11969000-11989600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr16:11969200-11990600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr16:11969400-11981800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr16:11969400-11986200	Strong transcription	Brain Anterior Caudate	brain
48	chr16:11969800-11981800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr16:11970200-11987800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr16:11970600-11985600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links