Variant report

Variant	rs11646545
Chromosome Location	chr16:11934594-11934595
allele	G/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:11891667..11893242-chr16:11933417..11935940,2	K562	blood:
2	chr16:11891274..11893242-chr16:11933417..11935378,2	K562	blood:
3	chr16:11926170..11928281-chr16:11932222..11935066,2	MCF-7	breast:
4	chr16:11934019..11936262-chr16:11938089..11940638,2	K562	blood:
5	chr16:11932400..11934949-chr16:11938294..11940166,4	MCF-7	breast:
6	chr16:11927874..11935119-chr16:11941272..11948071,15	MCF-7	breast:
7	chr16:11933587..11935992-chr16:11936964..11938745,3	K562	blood:
8	chr16:11932147..11934951-chr16:12152192..12155016,2	MCF-7	breast:
9	chr16:11927974..11933257-chr16:11934025..11938178,7	K562	blood:
10	chr16:11927858..11929755-chr16:11932603..11935135,2	MCF-7	breast:
11	chr16:11930789..11934327-chr16:11934498..11938238,6	MCF-7	breast:
12	chr16:11933188..11935979-chr16:11939785..11942257,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263307	Chromatin interaction
ENSG00000171490	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1019813	0.80[CEU][hapmap]
rs10744977	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10852344	0.80[CEU][hapmap]
rs11075022	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11075030	0.80[CEU][hapmap]
rs11075032	0.80[CEU][hapmap]
rs11647818	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11649405	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12925740	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs153025	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs154148	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs171656	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17235629	0.80[CEU][hapmap]
rs2075159	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2215928	0.80[CEU][hapmap]
rs251723	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28279	0.83[CEU][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33619	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs33623	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs33631	0.92[CEU][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs33637	0.87[AMR][1000 genomes]
rs33640	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs33643	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs33645	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs33647	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs33649	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs33651	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33652	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs33653	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33655	0.92[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33660	0.91[CEU][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35153773	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3971913	0.81[EUR][1000 genomes]
rs40311	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4429311	0.87[CEU][hapmap]
rs4493057	0.87[CEU][hapmap]
rs4511557	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs718081	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7185589	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7193470	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7196913	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7197111	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7198817	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7202234	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8046617	0.90[ASN][1000 genomes]
rs8047726	0.87[ASN][1000 genomes]
rs8061189	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[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	nsv482288	chr16:11776491-11946429	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
rs11646545	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	chr16:11918600-11943800	Weak transcription	Right Atrium	heart
2	chr16:11928400-11942000	Strong transcription	Primary T cells from cord blood	blood
3	chr16:11928800-11936600	Strong transcription	Primary B cells from cord blood	blood
4	chr16:11929200-11943000	Strong transcription	Lung	lung
5	chr16:11929200-11944000	Strong transcription	Fetal Stomach	stomach
6	chr16:11929400-11938000	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:11929400-11942200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr16:11929400-11942800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr16:11929400-11942800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:11929400-11943000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr16:11929400-11943000	Strong transcription	Fetal Intestine Small	intestine
12	chr16:11929400-11943200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr16:11929400-11943400	Strong transcription	Brain Germinal Matrix	brain
14	chr16:11929400-11943600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr16:11929400-11943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:11929600-11940800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr16:11929600-11941000	Strong transcription	Brain Hippocampus Middle	brain
18	chr16:11929600-11942600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr16:11929600-11942600	Strong transcription	Thymus	Thymus
20	chr16:11929600-11943000	Strong transcription	Rectal Smooth Muscle	rectum
21	chr16:11929600-11943200	Strong transcription	Brain Anterior Caudate	brain
22	chr16:11929600-11943200	Strong transcription	Fetal Brain Female	brain
23	chr16:11929600-11943200	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr16:11929600-11944000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr16:11929800-11942000	Strong transcription	Pancreas	Pancrea
26	chr16:11929800-11942400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr16:11929800-11943200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr16:11929800-11943400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr16:11929800-11943400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr16:11930000-11935800	Strong transcription	Brain Substantia Nigra	brain
31	chr16:11930000-11941000	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr16:11930000-11941400	Strong transcription	Ovary	ovary
33	chr16:11930000-11941600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr16:11930000-11941800	Strong transcription	Dnd41	blood
35	chr16:11930000-11942400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr16:11930000-11942400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr16:11930000-11942600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr16:11930000-11942800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr16:11930000-11942800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr16:11930000-11943000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr16:11930000-11943000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr16:11930000-11943200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr16:11930000-11943200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr16:11930000-11943400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr16:11930000-11943400	Strong transcription	Brain Angular Gyrus	brain
46	chr16:11930000-11943400	Strong transcription	Fetal Intestine Large	intestine
47	chr16:11930000-11943600	Strong transcription	Fetal Muscle Leg	muscle
48	chr16:11930000-11943800	Strong transcription	Liver	Liver
49	chr16:11930000-11944000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr16:11930000-11944000	Strong transcription	Monocytes-CD14+_RO01746	blood

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