Variant report

Variant	rs28688840
Chromosome Location	chr17:15605662-15605663
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2601951	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55748835	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9890896	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv457695	chr17:15447364-15611495	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv574462	chr17:15447364-15611495	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
7	nsv520426	chr17:15554561-15647723	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv518620	chr17:15563393-15608194	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv522564	chr17:15592762-15608194	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv962262	chr17:15601321-15609621	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28688840	ZNF286A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15603200-15606200	Weak transcription	Fetal Brain Male	brain
2	chr17:15603200-15608200	Weak transcription	Primary B cells from cord blood	blood
3	chr17:15603200-15609200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:15603400-15606800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr17:15603400-15607400	Weak transcription	Fetal Intestine Large	intestine
6	chr17:15603400-15607600	Weak transcription	Spleen	Spleen
7	chr17:15603400-15607800	Weak transcription	Esophagus	oesophagus
8	chr17:15603400-15608400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr17:15603400-15608400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr17:15603400-15608600	Weak transcription	Liver	Liver
11	chr17:15603400-15608600	Weak transcription	NHDF-Ad	bronchial
12	chr17:15603400-15608800	Weak transcription	Primary T cells from cord blood	blood
13	chr17:15603400-15609000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr17:15603400-15609000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr17:15603400-15609000	Weak transcription	Placenta	Placenta
16	chr17:15603400-15609200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr17:15603400-15609200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:15603400-15609200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:15603400-15609200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr17:15603400-15609200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:15603400-15609200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr17:15603400-15609200	Weak transcription	Fetal Kidney	kidney
23	chr17:15603400-15609200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:15603400-15609400	Weak transcription	Brain Anterior Caudate	brain
25	chr17:15603400-15609400	Weak transcription	Brain Substantia Nigra	brain
26	chr17:15603400-15609400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr17:15603400-15609600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr17:15603400-15609600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:15603400-15609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr17:15603400-15609600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:15603400-15609600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr17:15603400-15609600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr17:15603400-15609600	Weak transcription	Thymus	Thymus
34	chr17:15603400-15609600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr17:15603400-15609800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr17:15603400-15609800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr17:15603400-15610200	Weak transcription	Aorta	Aorta
38	chr17:15603400-15610200	Weak transcription	Left Ventricle	heart
39	chr17:15603400-15610200	Weak transcription	Lung	lung
40	chr17:15603400-15610400	Weak transcription	Gastric	stomach
41	chr17:15603400-15610800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr17:15603400-15610800	Weak transcription	Adipose Nuclei	Adipose
43	chr17:15603400-15610800	Weak transcription	Psoas Muscle	Psoas
44	chr17:15603400-15610800	Weak transcription	NHLF	lung
45	chr17:15603400-15611000	Weak transcription	Brain Angular Gyrus	brain
46	chr17:15603400-15611000	Weak transcription	Right Ventricle	heart
47	chr17:15603400-15611600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr17:15603400-15612000	Weak transcription	Colon Smooth Muscle	Colon
49	chr17:15603400-15616400	Weak transcription	Pancreas	Pancrea
50	chr17:15603600-15607600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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