Variant report

Variant	rs7825914
Chromosome Location	chr8:19590012-19590013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD3-3	chr8:19589967-19590077	NONHSAT125379

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1027265	0.99[ASN][1000 genomes]
rs6586861	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981526	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984390	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6999473	0.91[ASN][1000 genomes]
rs7820737	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7831059	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7831332	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7837392	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7842223	0.91[ASN][1000 genomes]
rs9644633	0.97[ASN][1000 genomes]
rs9650598	0.91[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	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
2	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
3	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
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv3478971	chr8:19587201-19591233	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv3478972	chr8:19587201-19591233	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	esv19364	chr8:19587584-19590311	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv610760	chr8:19588133-19590218	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7825914	ChGn	cis	multi-tissue	Pritchard
rs7825914	TMEM90B	trans	parietal	SCAN
rs7825914	NKX3-1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19575400-19596800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr8:19576400-19591800	Weak transcription	Primary B cells from cord blood	blood
3	chr8:19577800-19599000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr8:19578200-19591400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:19583600-19592400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr8:19585400-19591200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:19587400-19597000	Weak transcription	Brain Hippocampus Middle	brain
8	chr8:19587400-19602800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr8:19587600-19591600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr8:19587600-19600800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr8:19588400-19590200	Enhancers	Fetal Heart	heart
12	chr8:19588400-19591000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr8:19588600-19590400	Genic enhancers	A549	lung
14	chr8:19588600-19613400	Weak transcription	Pancreas	Pancrea
15	chr8:19588800-19596400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr8:19589000-19590200	Enhancers	Fetal Lung	lung
17	chr8:19589000-19591000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:19589000-19591000	Weak transcription	Left Ventricle	heart
19	chr8:19589000-19591000	Weak transcription	Right Atrium	heart
20	chr8:19589200-19591000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr8:19589200-19591000	Weak transcription	Right Ventricle	heart
22	chr8:19589200-19592200	Enhancers	Hela-S3	cervix
23	chr8:19589600-19590200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr8:19589600-19590800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr8:19589600-19591200	Enhancers	Fetal Brain Female	brain
26	chr8:19589600-19591200	Weak transcription	Placenta	Placenta
27	chr8:19589800-19590200	Enhancers	Osteobl	bone
28	chr8:19589800-19590400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:19589800-19590400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:19589800-19590400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr8:19590000-19590600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr8:19590000-19591000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:19590000-19591200	Enhancers	Primary T cells from cord blood	blood

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