Variant report

Variant	rs33655
Chromosome Location	chr16:11970381-11970382
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	chr16:11768134..11770155-chr16:11969703..11971604,2	MCF-7	breast:
2	chr16:11968165..11970950-chr16:11974368..11976802,2	K562	blood:

Variant related genes	Relation type
ENSG00000261560	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11075022	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11570136	0.81[CEU][hapmap]
rs11646545	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]
rs11647818	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11649405	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12925740	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs153025	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs154148	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs171656	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2018199	0.88[CEU][hapmap]
rs2075158	0.88[CEU][hapmap]
rs2075159	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs251723	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28279	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33620	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33635	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs33637	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33640	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33643	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33645	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33647	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33648	0.84[EUR][1000 genomes]
rs33649	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33651	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33652	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33653	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33654	0.84[EUR][1000 genomes]
rs33660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35153773	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs40311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42424	0.82[EUR][1000 genomes]
rs4429311	0.81[CEU][hapmap]
rs4493057	0.80[CEU][hapmap]
rs4511557	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs456325	0.85[CEU][hapmap]
rs718081	0.89[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs7185589	0.85[ASN][1000 genomes]
rs7193470	0.81[ASN][1000 genomes]
rs7197111	0.81[AMR][1000 genomes]
rs7198817	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7202234	0.92[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8046617	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8047726	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8059891	0.85[CEU][hapmap]
rs8061189	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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
rs33655	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	chr16:11946200-11975600	Weak transcription	Aorta	Aorta
2	chr16:11946400-11975600	Weak transcription	Esophagus	oesophagus
3	chr16:11946600-11970400	Weak transcription	Right Atrium	heart
4	chr16:11961200-11972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr16:11961400-11975600	Weak transcription	Pancreas	Pancrea
6	chr16:11961600-11971600	Strong transcription	NHDF-Ad	bronchial
7	chr16:11961600-11986000	Weak transcription	Stomach Mucosa	stomach
8	chr16:11961800-11972400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr16:11961800-11991000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:11962000-11992200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr16:11962000-11994600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr16:11962200-11992000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr16:11962400-11971800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr16:11962400-11972800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr16:11962400-11982600	Strong transcription	Fetal Thymus	thymus
16	chr16:11962400-11984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr16:11962400-11990800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:11962400-11992000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr16:11962400-11992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:11962400-11992200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr16:11962400-11992400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr16:11962400-11995000	Strong transcription	Dnd41	blood
23	chr16:11962600-11971200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr16:11962600-11985600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr16:11962600-11990600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr16:11962600-11991800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr16:11962600-12004000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:11963000-11971000	Strong transcription	Hela-S3	cervix
29	chr16:11963200-11970800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr16:11963400-11972600	Strong transcription	K562	blood
31	chr16:11963400-11975000	Weak transcription	Fetal Kidney	kidney
32	chr16:11963800-11970400	Weak transcription	Fetal Brain Female	brain
33	chr16:11963800-11974000	Weak transcription	Fetal Brain Male	brain
34	chr16:11963800-11976000	Weak transcription	HSMMtube	muscle
35	chr16:11964600-11970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr16:11964800-11971600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr16:11964800-11990800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr16:11964800-11991000	Strong transcription	Fetal Intestine Large	intestine
39	chr16:11965000-11974200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr16:11965000-11986400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr16:11965000-11990200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:11965000-11991000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr16:11965200-11971200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr16:11965200-11991000	Strong transcription	GM12878-XiMat	blood
45	chr16:11965400-11990800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr16:11965400-11991400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr16:11965600-11971600	Strong transcription	HMEC	breast
48	chr16:11965600-11983000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr16:11965600-11983200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr16:11965600-11991000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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