Variant report

Variant	rs153025
Chromosome Location	chr16:11957930-11957931
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:11947083..11948628-chr16:11955967..11958698,2	K562	blood:
2	chr16:11952846..11955824-chr16:11956865..11960042,4	K562	blood:
3	chr16:11944988..11947048-chr16:11957743..11959952,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171490	Chromatin interaction
ENSG00000263307	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11075022	0.83[AMR][1000 genomes]
rs11646545	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11647818	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11649405	0.83[AMR][1000 genomes]
rs12925740	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs154148	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs171656	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075159	0.86[EUR][1000 genomes]
rs251723	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28279	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33619	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33620	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33623	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33631	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33637	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33640	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33643	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33645	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33647	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33648	0.81[EUR][1000 genomes]
rs33649	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33651	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33652	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33653	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33654	0.82[EUR][1000 genomes]
rs33655	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33660	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35153773	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs40311	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4511557	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs718081	0.83[AMR][1000 genomes]
rs7185589	0.84[ASN][1000 genomes]
rs7198817	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7202234	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8046617	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8047726	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8061189	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs153025	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11946200-11975600	Weak transcription	Aorta	Aorta
2	chr16:11946400-11969400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:11946400-11969400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr16:11946400-11969400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:11946400-11975600	Weak transcription	Esophagus	oesophagus
6	chr16:11946600-11958400	Weak transcription	Psoas Muscle	Psoas
7	chr16:11946600-11959600	Weak transcription	NHLF	lung
8	chr16:11946600-11961200	Weak transcription	Stomach Mucosa	stomach
9	chr16:11946600-11961400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:11946600-11961400	Weak transcription	Fetal Kidney	kidney
11	chr16:11946600-11961400	Weak transcription	HSMM	muscle
12	chr16:11946600-11961800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:11946600-11961800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr16:11946600-11961800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr16:11946600-11962000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:11946600-11962200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr16:11946600-11962400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr16:11946600-11962400	Weak transcription	HSMMtube	muscle
19	chr16:11946600-11966800	Weak transcription	Lung	lung
20	chr16:11946600-11969000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:11946600-11970400	Weak transcription	Right Atrium	heart
22	chr16:11946800-11962000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr16:11946800-11962200	Weak transcription	Thymus	Thymus
24	chr16:11947000-11961800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr16:11947000-11962000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr16:11947000-11962000	Weak transcription	Fetal Muscle Leg	muscle
27	chr16:11947000-11962400	Weak transcription	Fetal Intestine Large	intestine
28	chr16:11947000-11969400	Weak transcription	Right Ventricle	heart
29	chr16:11947200-11960000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr16:11947200-11966800	Weak transcription	Small Intestine	intestine
31	chr16:11947200-11967200	Weak transcription	Fetal Intestine Small	intestine
32	chr16:11947200-11967200	Weak transcription	Fetal Stomach	stomach
33	chr16:11947200-11968800	Weak transcription	Ovary	ovary
34	chr16:11948000-11961600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr16:11948000-11962600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:11948000-11963400	Weak transcription	Spleen	Spleen
37	chr16:11948200-11959400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr16:11948200-11960600	Weak transcription	Pancreas	Pancrea
39	chr16:11948200-11961200	Weak transcription	NHEK	skin
40	chr16:11948200-11962200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr16:11948200-11962400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr16:11948400-11962400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr16:11948400-11962400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr16:11948400-11963200	Weak transcription	Fetal Lung	lung
45	chr16:11948400-11969000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:11948600-11959400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr16:11948600-11961400	Weak transcription	Primary T cells from cord blood	blood
48	chr16:11948600-11962000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr16:11948600-11962200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr16:11948600-11962200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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