Variant report

Variant	rs33621
Chromosome Location	chr16:12008513-12008514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:11886565..11889362-chr16:12006902..12008695,2	K562	blood:
2	chr16:12008410..12010246-chr16:15742278..15744306,2	MCF-7	breast:
3	chr16:11942158..11945019-chr16:12007276..12009748,2	K562	blood:
4	chr10:124133719..124134527-chr16:12008397..12008926,2	Hela-S3	cervix:
5	chr16:12008162..12010269-chr16:12142729..12146819,3	K562	blood:
6	chr16:11941713..11946689-chr16:12006948..12011249,6	MCF-7	breast:
7	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:
8	chr16:11944315..11946480-chr16:12008232..12011350,3	K562	blood:
9	chr16:11988764..11995180-chr16:12006980..12012068,9	MCF-7	breast:
10	chr16:12007951..12010484-chr17:59476175..59479111,2	MCF-7	breast:
11	chr16:12008413..12010461-chr16:12056035..12059014,2	MCF-7	breast:
12	chr16:11831944..11836692-chr16:12007199..12011492,4	K562	blood:
13	chr16:11943912..11945965-chr16:12008319..12011491,4	MCF-7	breast:
14	chr16:12006809..12011472-chr16:12069677..12072698,7	MCF-7	breast:
15	chr16:12007765..12009301-chr16:12009316..12010905,2	MCF-7	breast:
16	chr16:11988100..11996073-chr16:12007143..12011577,10	MCF-7	breast:
17	chr16:12007711..12010113-chr16:12069770..12071913,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000262420	Chromatin interaction
ENSG00000153066	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000048462	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000072864	Chromatin interaction
ENSG00000107679	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000234719	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000260488	Chromatin interaction
ENSG00000171490	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000263307	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs190461	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018199	0.81[EUR][1000 genomes]
rs2075158	0.82[EUR][1000 genomes]
rs256400	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs33619	0.85[EUR][1000 genomes]
rs33620	0.85[EUR][1000 genomes]
rs33623	0.85[EUR][1000 genomes]
rs33624	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33629	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33630	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33631	0.80[EUR][1000 genomes]
rs33635	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33638	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33648	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33654	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs42424	0.90[EUR][1000 genomes]
rs456325	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052900	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv974848	chr16:12005053-12020022	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
5	esv3410856	chr16:12007876-12010424	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
6	esv3518112	chr16:12008201-12011049	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
7	esv3518113	chr16:12008201-12011049	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
8	esv3408224	chr16:12008276-12010824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33621	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12006200-12008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:12006200-12008600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:12006200-12008600	Transcr. at gene 5' and 3'	K562	blood
4	chr16:12006600-12008600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr16:12006600-12010400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:12006800-12008600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:12006800-12008600	Flanking Active TSS	HUVEC	blood vessel
8	chr16:12006800-12009000	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr16:12007000-12008600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:12007000-12008600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr16:12007000-12009000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr16:12007200-12008600	Flanking Active TSS	Liver	Liver
13	chr16:12007200-12008600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr16:12007200-12008600	Transcr. at gene 5' and 3'	NHEK	skin
15	chr16:12007200-12008800	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr16:12007200-12009000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:12007200-12010400	Active TSS	Right Atrium	heart
18	chr16:12007200-12010600	Active TSS	A549	lung
19	chr16:12007400-12008600	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr16:12007400-12008600	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr16:12007400-12008600	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr16:12007400-12008600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr16:12007400-12008600	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr16:12007400-12008800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr16:12007400-12008800	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr16:12007400-12009000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr16:12007400-12009200	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr16:12007400-12009800	Active TSS	GM12878-XiMat	blood
29	chr16:12007400-12010200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr16:12007400-12010200	Active TSS	HSMMtube	muscle
31	chr16:12007400-12010600	Active TSS	Esophagus	oesophagus
32	chr16:12007400-12010800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr16:12007600-12008600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr16:12007600-12008600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr16:12007600-12008600	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr16:12007600-12008800	Flanking Active TSS	Fetal Lung	lung
37	chr16:12007600-12010000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:12007600-12010400	Active TSS	Left Ventricle	heart
39	chr16:12007600-12010600	Active TSS	Aorta	Aorta
40	chr16:12007800-12008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr16:12007800-12008600	Weak transcription	Gastric	stomach
42	chr16:12007800-12008600	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr16:12007800-12008800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr16:12007800-12008800	Flanking Active TSS	Fetal Brain Female	brain
45	chr16:12007800-12009000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr16:12007800-12009200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr16:12007800-12010000	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr16:12007800-12010200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:12007800-12010200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr16:12007800-12010200	Active TSS	Primary T helper naive cells from peripheral blood	blood

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