Variant report

Variant	rs17128520
Chromosome Location	chr8:19363592-19363593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD3-3	chr8:19363417-19363641	NONHSAT125377
2	lnc-PSD3-3	chr8:19363391-19363641	NONHSAT125376
3	lnc-PSD3-3	chr8:19363548-19363641	NONHSAT125378

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10087317	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10087663	1.00[AMR][1000 genomes]
rs10088450	1.00[AMR][1000 genomes]
rs10090079	0.82[YRI][hapmap];0.91[AFR][1000 genomes]
rs10094142	1.00[AMR][1000 genomes]
rs10096485	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10096490	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10096638	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10096712	1.00[YRI][hapmap]
rs10097851	1.00[AMR][1000 genomes]
rs10098690	1.00[YRI][hapmap]
rs10101907	1.00[AMR][1000 genomes]
rs10104266	1.00[YRI][hapmap]
rs10104615	1.00[AMR][1000 genomes]
rs10104968	1.00[AMR][1000 genomes]
rs10105670	1.00[YRI][hapmap]
rs10106180	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10106270	1.00[AMR][1000 genomes]
rs10107181	1.00[AMR][1000 genomes]
rs10109345	1.00[AMR][1000 genomes]
rs10156383	1.00[YRI][hapmap]
rs10216575	1.00[YRI][hapmap]
rs10216916	1.00[YRI][hapmap]
rs10481442	0.91[AFR][1000 genomes]
rs13328370	1.00[YRI][hapmap]
rs17128428	0.91[AFR][1000 genomes]
rs17128532	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17128535	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17128545	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17128641	1.00[AMR][1000 genomes]
rs17128662	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17128691	1.00[AMR][1000 genomes]
rs17128714	1.00[AMR][1000 genomes]
rs17128743	1.00[AMR][1000 genomes]
rs17128745	1.00[AMR][1000 genomes]
rs28415838	1.00[AMR][1000 genomes]
rs28427117	1.00[AMR][1000 genomes]
rs28457744	1.00[AMR][1000 genomes]
rs28491635	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28558362	0.91[AFR][1000 genomes]
rs28578312	1.00[AMR][1000 genomes]
rs28607676	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28661517	1.00[AMR][1000 genomes]
rs28713671	1.00[AMR][1000 genomes]
rs28738093	1.00[AMR][1000 genomes]
rs28742998	1.00[AMR][1000 genomes]
rs28872331	0.82[AFR][1000 genomes]
rs7817946	1.00[AMR][1000 genomes]
rs7821215	1.00[AMR][1000 genomes]
rs7821389	1.00[AMR][1000 genomes]
rs7821612	1.00[AMR][1000 genomes]
rs7824941	1.00[AMR][1000 genomes]
rs7839912	1.00[AMR][1000 genomes]
rs7840172	1.00[AMR][1000 genomes]
rs7843893	1.00[AMR][1000 genomes]
rs9325858	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv890623	chr8:19307051-19383697	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv890624	chr8:19319061-19456270	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19338800-19370600	Weak transcription	Esophagus	oesophagus
2	chr8:19348000-19376600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:19348200-19364000	Weak transcription	Brain Hippocampus Middle	brain
4	chr8:19348200-19367400	Weak transcription	Fetal Brain Female	brain
5	chr8:19351200-19369000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr8:19353400-19367600	Weak transcription	Brain Anterior Caudate	brain
7	chr8:19353400-19367600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr8:19354400-19367800	Weak transcription	Brain Substantia Nigra	brain
9	chr8:19354800-19366000	Weak transcription	Brain Angular Gyrus	brain
10	chr8:19355800-19367600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:19356000-19368400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:19356400-19368600	Weak transcription	Thymus	Thymus
13	chr8:19358000-19365000	Strong transcription	Primary B cells from cord blood	blood
14	chr8:19358200-19364200	Weak transcription	Hela-S3	cervix
15	chr8:19358400-19363800	Weak transcription	Osteobl	bone
16	chr8:19359000-19364200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr8:19359800-19367800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr8:19360800-19363800	Weak transcription	Brain Germinal Matrix	brain
19	chr8:19360800-19364800	Strong transcription	A549	lung
20	chr8:19361000-19365600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr8:19361400-19363800	Transcr. at gene 5' and 3'	Placenta	Placenta
22	chr8:19361400-19364000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:19361600-19363800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr8:19362000-19364400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr8:19362000-19364400	Enhancers	NHDF-Ad	bronchial
26	chr8:19362000-19364600	Enhancers	Fetal Lung	lung
27	chr8:19362200-19363800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr8:19362200-19364200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr8:19362400-19363600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr8:19362600-19363600	Bivalent Enhancer	Fetal Stomach	stomach
31	chr8:19362600-19364400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr8:19362600-19364600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr8:19362600-19364600	Enhancers	Fetal Muscle Leg	muscle
34	chr8:19362800-19363800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr8:19362800-19363800	Bivalent Enhancer	Fetal Thymus	thymus
36	chr8:19362800-19364400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:19362800-19364800	Enhancers	Right Atrium	heart
38	chr8:19362800-19368400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr8:19363000-19363600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr8:19363000-19364000	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr8:19363000-19364200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr8:19363000-19365000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr8:19363000-19369600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr8:19363000-19372600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr8:19363200-19363600	Enhancers	Primary hematopoietic stem cells	blood
46	chr8:19363200-19363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr8:19363200-19363600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr8:19363200-19364200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr8:19363200-19364200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr8:19363200-19364200	Weak transcription	Adipose Nuclei	Adipose

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