Variant report

Variant	rs33630
Chromosome Location	chr16:11996006-11996007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:11988100..11996073-chr16:12007143..12011577,10	MCF-7	breast:
2	chr16:11995805..11997895-chr16:11999414..12002244,2	MCF-7	breast:
3	chr16:11981260..11984239-chr16:11994473..11997426,2	K562	blood:

Variant related genes	Relation type
ENSG00000103342	Chromatin interaction
ENSG00000261216	Chromatin interaction
ENSG00000266163	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12924398	0.81[ASN][1000 genomes]
rs190461	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2018199	0.82[EUR][1000 genomes]
rs2075158	0.83[EUR][1000 genomes]
rs256400	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs33621	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33624	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33629	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33631	0.82[EUR][1000 genomes]
rs33635	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33637	0.80[EUR][1000 genomes]
rs33638	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33640	0.80[EUR][1000 genomes]
rs33648	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33654	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42424	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs456325	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8052900	0.81[EUR][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	nsv1735	chr16:11986963-12031597	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33630	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr16:11966200-12006200	Weak transcription	Fetal Heart	heart
3	chr16:11976600-12004800	Weak transcription	Esophagus	oesophagus
4	chr16:11977000-12007200	Weak transcription	Colonic Mucosa	Colon
5	chr16:11977200-12004600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr16:11979800-12003200	Weak transcription	Small Intestine	intestine
7	chr16:11981200-12004000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr16:11981800-12001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr16:11982000-12007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:11984600-12006800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:11985000-12007000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr16:11986200-11996400	Weak transcription	Spleen	Spleen
13	chr16:11986200-11999600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr16:11986200-12003800	Weak transcription	Brain Substantia Nigra	brain
15	chr16:11987600-12004000	Weak transcription	Brain Angular Gyrus	brain
16	chr16:11987800-11996600	Weak transcription	Right Ventricle	heart
17	chr16:11987800-12004200	Weak transcription	Fetal Brain Female	brain
18	chr16:11987800-12007600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr16:11987800-12008400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:11988000-12004200	Weak transcription	Fetal Kidney	kidney
21	chr16:11988200-12000000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr16:11989200-11996800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr16:11989200-12004000	Weak transcription	Fetal Lung	lung
24	chr16:11989600-12000200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr16:11989800-11997000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr16:11989800-11999200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:11989800-12000000	Weak transcription	Ovary	ovary
28	chr16:11989800-12007200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr16:11989800-12007400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr16:11990000-12001000	Weak transcription	Fetal Muscle Leg	muscle
31	chr16:11990000-12007400	Weak transcription	Lung	lung
32	chr16:11990600-11996800	Weak transcription	Fetal Intestine Small	intestine
33	chr16:11990600-12004200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr16:11990600-12006600	Weak transcription	Brain Germinal Matrix	brain
35	chr16:11990800-11996800	Weak transcription	Fetal Stomach	stomach
36	chr16:11990800-11998600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr16:11990800-12001200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr16:11990800-12007000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr16:11991000-11996800	Weak transcription	Fetal Thymus	thymus
40	chr16:11991000-11997000	Weak transcription	Fetal Intestine Large	intestine
41	chr16:11991000-11997200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr16:11991000-11997200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr16:11991000-11998400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr16:11991000-11999400	Weak transcription	Thymus	Thymus
45	chr16:11991000-12002800	Weak transcription	Adipose Nuclei	Adipose
46	chr16:11991000-12003000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr16:11991000-12004200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr16:11991000-12004200	Weak transcription	Brain Hippocampus Middle	brain
49	chr16:11991000-12006800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr16:11991000-12007400	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links