Variant report

Variant	rs33640
Chromosome Location	chr16:11986874-11986875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:11944038..11947076-chr16:11983498..11987330,3	MCF-7	breast:
2	chr16:11986091..11989126-chr16:11998045..12000839,3	K562	blood:

Variant related genes	Relation type
ENSG00000263307	Chromatin interaction
ENSG00000171490	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11075022	0.84[AMR][1000 genomes]
rs11646545	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11647818	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11649405	0.84[AMR][1000 genomes]
rs12925740	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153025	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs154148	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171656	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2075159	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs251723	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28279	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33619	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33620	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33623	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33629	0.82[EUR][1000 genomes]
rs33630	0.80[EUR][1000 genomes]
rs33631	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33635	0.85[EUR][1000 genomes]
rs33637	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33643	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33645	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33647	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33648	0.83[EUR][1000 genomes]
rs33649	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33651	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33652	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33653	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33654	0.80[EUR][1000 genomes]
rs33655	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33660	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35153773	0.84[AMR][1000 genomes]
rs40311	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs42424	0.81[EUR][1000 genomes]
rs4511557	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs718081	0.84[AMR][1000 genomes]
rs7197111	0.81[AMR][1000 genomes]
rs7198817	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7202234	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8046617	0.85[ASN][1000 genomes]
rs8047726	0.82[ASN][1000 genomes]
rs8061189	0.92[AMR][1000 genomes];0.93[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	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
rs33640	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	chr16:11961800-11991000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr16:11962000-11992200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr16:11962000-11994600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:11962200-11992000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr16:11962400-11990800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr16:11962400-11995000	Strong transcription	Dnd41	blood
11	chr16:11962600-11990600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:11962600-11991800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:11964800-11990800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:11964800-11991000	Strong transcription	Fetal Intestine Large	intestine
16	chr16:11965000-11990200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr16:11965000-11991000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr16:11965200-11991000	Strong transcription	GM12878-XiMat	blood
19	chr16:11965400-11990800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr16:11965400-11991400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr16:11965600-11991000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:11965800-11990200	Strong transcription	Liver	Liver
23	chr16:11965800-11995000	Strong transcription	HepG2	liver
24	chr16:11966000-11991000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr16:11966000-11991400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:11966200-11989400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr16:11966200-12006200	Weak transcription	Fetal Heart	heart
28	chr16:11966600-11988200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr16:11966600-11991000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr16:11967000-11990200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr16:11969000-11989600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr16:11969200-11990600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr16:11970200-11987800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr16:11971600-11995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr16:11972000-11990400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr16:11972000-11991000	Strong transcription	Thymus	Thymus
37	chr16:11972200-11989600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr16:11972400-11991000	Strong transcription	Adipose Nuclei	Adipose
39	chr16:11973000-11990400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr16:11973200-11989600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr16:11973400-11990200	Strong transcription	Osteobl	bone
42	chr16:11973600-11989200	Strong transcription	Fetal Lung	lung
43	chr16:11973600-11990400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr16:11973800-11988200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr16:11973800-11991000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr16:11973800-11991000	Strong transcription	Primary T cells from cord blood	blood
47	chr16:11974400-11990000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:11974600-11991200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr16:11976000-11987400	Weak transcription	Aorta	Aorta
50	chr16:11976600-12004800	Weak transcription	Esophagus	oesophagus

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