Variant report

Variant	rs33647
Chromosome Location	chr16:11982982-11982983
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:11958981..11960490-chr16:11981587..11984352,2	MCF-7	breast:
2	chr16:11981260..11984239-chr16:11994473..11997426,2	K562	blood:
3	chr16:11982694..11985676-chr16:12003356..12006033,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11075022	0.84[AMR][1000 genomes]
rs11646545	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11647818	0.87[AMR][1000 genomes]
rs11649405	0.84[AMR][1000 genomes]
rs12925740	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs153025	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs154148	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs171656	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2075159	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs251723	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28279	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33619	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33620	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33623	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33631	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33635	0.82[EUR][1000 genomes]
rs33637	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33640	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33643	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33645	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33648	0.85[EUR][1000 genomes]
rs33649	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33651	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33652	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33653	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33654	0.82[EUR][1000 genomes]
rs33655	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33660	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153773	0.84[AMR][1000 genomes]
rs40311	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs42424	0.83[EUR][1000 genomes]
rs4511557	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs718081	0.84[AMR][1000 genomes]
rs7197111	0.81[AMR][1000 genomes]
rs7198817	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7202234	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8046617	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8061189	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[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
rs33647	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	chr16:11962400-11984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:11962400-11990800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr16:11962400-11995000	Strong transcription	Dnd41	blood
13	chr16:11962600-11985600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:11962600-11990600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr16:11962600-11991800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:11964800-11990800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:11964800-11991000	Strong transcription	Fetal Intestine Large	intestine
19	chr16:11965000-11986400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr16:11965000-11990200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr16:11965000-11991000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr16:11965200-11991000	Strong transcription	GM12878-XiMat	blood
23	chr16:11965400-11990800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr16:11965400-11991400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr16:11965600-11983000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr16:11965600-11983200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr16:11965600-11991000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr16:11965800-11990200	Strong transcription	Liver	Liver
29	chr16:11965800-11995000	Strong transcription	HepG2	liver
30	chr16:11966000-11991000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:11966000-11991400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr16:11966200-11984200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:11966200-11989400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr16:11966200-12006200	Weak transcription	Fetal Heart	heart
35	chr16:11966600-11983800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr16:11966600-11988200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr16:11966600-11991000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr16:11967000-11990200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:11969000-11984600	Strong transcription	Fetal Muscle Leg	muscle
40	chr16:11969000-11989600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:11969200-11990600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:11969400-11986200	Strong transcription	Brain Anterior Caudate	brain
43	chr16:11970200-11987800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr16:11970600-11985600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:11971600-11995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr16:11972000-11990400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr16:11972000-11991000	Strong transcription	Thymus	Thymus
48	chr16:11972200-11989600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr16:11972400-11991000	Strong transcription	Adipose Nuclei	Adipose
50	chr16:11972600-11986200	Strong transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links