Variant report

Variant	rs9936589
Chromosome Location	chr16:69884817-69884818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10852460	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852461	0.83[ASN][1000 genomes]
rs11075742	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075744	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1116544	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11642008	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11645565	0.85[AMR][1000 genomes]
rs11648348	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12927168	0.85[EUR][1000 genomes]
rs1466863	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1500337	0.87[ASN][1000 genomes]
rs1566453	0.83[ASN][1000 genomes]
rs1566454	0.87[ASN][1000 genomes]
rs1566456	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2133799	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2362642	0.83[ASN][1000 genomes]
rs3790075	0.87[ASN][1000 genomes]
rs3790076	0.87[ASN][1000 genomes]
rs3790080	0.87[ASN][1000 genomes]
rs3790082	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790083	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985447	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985448	0.87[ASN][1000 genomes]
rs4985449	0.87[ASN][1000 genomes]
rs4985450	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55887947	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6499263	0.92[ASN][1000 genomes]
rs6499265	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6499268	0.87[ASN][1000 genomes]
rs7190013	0.87[ASN][1000 genomes]
rs7196917	0.87[AMR][1000 genomes]
rs7200258	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7202233	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8047194	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8047682	0.83[ASN][1000 genomes]
rs8048550	0.94[ASN][1000 genomes]
rs8049373	0.83[ASN][1000 genomes]
rs8050414	0.92[ASN][1000 genomes]
rs8050516	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8051168	0.98[ASN][1000 genomes]
rs8060478	0.83[ASN][1000 genomes]
rs8063226	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9927967	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9936723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9936589	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69834200-69892200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr16:69837000-69905600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr16:69852000-69893200	Weak transcription	K562	blood
5	chr16:69865000-69887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr16:69867000-69888400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr16:69868000-69885000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:69868000-69888800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr16:69868200-69885400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr16:69868200-69892800	Weak transcription	A549	lung
11	chr16:69868800-69888400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr16:69871200-69885000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr16:69873400-69888000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr16:69874000-69905800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr16:69874200-69889400	Weak transcription	Right Ventricle	heart
16	chr16:69874800-69887200	Weak transcription	Aorta	Aorta
17	chr16:69875200-69890600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:69875800-69886000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr16:69875800-69888800	Strong transcription	Fetal Intestine Small	intestine
20	chr16:69876000-69895000	Weak transcription	Fetal Brain Female	brain
21	chr16:69876000-69904400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr16:69876000-69905800	Weak transcription	Dnd41	blood
23	chr16:69876200-69885800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr16:69876200-69905800	Weak transcription	Brain Germinal Matrix	brain
25	chr16:69877000-69892400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr16:69877200-69892400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr16:69877600-69892200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:69879400-69885400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:69879400-69891600	Weak transcription	Thymus	Thymus
30	chr16:69879600-69886600	Weak transcription	Primary B cells from cord blood	blood
31	chr16:69879600-69887000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr16:69879600-69887200	Weak transcription	Esophagus	oesophagus
33	chr16:69879600-69887400	Weak transcription	GM12878-XiMat	blood
34	chr16:69879600-69887600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr16:69879600-69892200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr16:69879800-69892200	Weak transcription	Liver	Liver
37	chr16:69879800-69892200	Weak transcription	Fetal Thymus	thymus
38	chr16:69879800-69895000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr16:69880400-69887400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr16:69880400-69892200	Weak transcription	Hela-S3	cervix
41	chr16:69880600-69886600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr16:69881600-69890200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr16:69881800-69886200	Enhancers	Colon Smooth Muscle	Colon
44	chr16:69882000-69887200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr16:69882400-69887400	Weak transcription	Spleen	Spleen
46	chr16:69882800-69894800	Weak transcription	Colonic Mucosa	Colon
47	chr16:69883000-69893200	Weak transcription	Psoas Muscle	Psoas
48	chr16:69883000-69899400	Weak transcription	NHLF	lung
49	chr16:69883200-69885200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:69883200-69885200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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