Variant report

Variant	rs57288594
Chromosome Location	chr16:12239900-12239901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11075050	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11075051	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11075052	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11640920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11641707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11643720	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11647573	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12596036	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12596081	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12596229	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12597440	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12597662	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16958983	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4074264	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55693041	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55906538	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55925548	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55937851	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55975708	0.81[AMR][1000 genomes]
rs56058313	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56225320	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58198539	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59506769	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59855210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6498266	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7189640	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7190611	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73519857	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8051768	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8053242	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1039590	chr16:12237623-12279574	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12213800-12255400	Weak transcription	Gastric	stomach
2	chr16:12215400-12241600	Weak transcription	NH-A	brain
3	chr16:12217800-12241800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:12218600-12241200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr16:12218800-12241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr16:12221600-12241600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr16:12222000-12240800	Weak transcription	Brain Anterior Caudate	brain
8	chr16:12227600-12247000	Weak transcription	Colon Smooth Muscle	Colon
9	chr16:12228600-12240800	Weak transcription	HSMM	muscle
10	chr16:12228600-12241400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr16:12228600-12243600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr16:12228800-12240800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr16:12229000-12249000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:12229200-12241000	Weak transcription	Fetal Kidney	kidney
15	chr16:12229400-12240800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr16:12229400-12241000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr16:12229400-12241200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr16:12229400-12242800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr16:12229400-12248000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr16:12229400-12250600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr16:12229800-12241400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr16:12229800-12241400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr16:12229800-12244400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr16:12229800-12251400	Weak transcription	NHEK	skin
25	chr16:12229800-12253600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr16:12230000-12240800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:12230000-12245600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr16:12230200-12241200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr16:12230200-12241800	Weak transcription	Esophagus	oesophagus
30	chr16:12230200-12242000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr16:12230200-12256200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr16:12230600-12240800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr16:12231400-12241600	Weak transcription	Psoas Muscle	Psoas
34	chr16:12231400-12251000	Weak transcription	Ovary	ovary
35	chr16:12231400-12268000	Weak transcription	Pancreas	Pancrea
36	chr16:12231800-12241000	Weak transcription	Fetal Brain Female	brain
37	chr16:12232000-12241000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr16:12232000-12248600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr16:12233400-12241000	Weak transcription	Adipose Nuclei	Adipose
40	chr16:12233600-12241200	Weak transcription	Thymus	Thymus
41	chr16:12233600-12241400	Weak transcription	Fetal Thymus	thymus
42	chr16:12233600-12241400	Weak transcription	Spleen	Spleen
43	chr16:12233600-12251000	Weak transcription	NHDF-Ad	bronchial
44	chr16:12233800-12240800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr16:12234600-12241200	Weak transcription	Fetal Stomach	stomach
46	chr16:12234600-12241400	Weak transcription	Placenta	Placenta
47	chr16:12234600-12244000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr16:12234600-12247600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr16:12234600-12248600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr16:12234600-12261600	Weak transcription	Aorta	Aorta

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