Variant report

Variant	rs325380
Chromosome Location	chr15:100256618-100256619
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYSMD4-1	chr15:100255902-100258027	NONHSAT050878
2	lnc-LYSMD4-1	chr15:100255906-100258027	NONHSAT050879

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11247123	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1808723	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs2061007	0.92[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2862867	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs325400	0.84[JPT][hapmap]
rs882176	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
7	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv904563	chr15:100239546-100274747	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv570730	chr15:100240910-100700520	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
11	nsv1045838	chr15:100243067-101032218	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv904564	chr15:100245296-100723798	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv932678	chr15:100250311-101012358	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs325380	SPATA8	cis	cerebellum	SCAN
rs325380	LYSMD4	cis	parietal	SCAN
rs325380	LYSMD4	cis	Thyroid	GTEx
rs325380	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100244600-100272400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:100245000-100258200	Weak transcription	Fetal Kidney	kidney
3	chr15:100245600-100258000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:100246200-100257000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr15:100246400-100257400	Strong transcription	Primary B cells from cord blood	blood
6	chr15:100246600-100257400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:100246800-100259000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:100247000-100258600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:100247200-100256800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:100248400-100259600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:100248400-100260000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:100248800-100258000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:100249000-100259600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:100249200-100257200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:100249200-100257200	Strong transcription	Thymus	Thymus
16	chr15:100249200-100259600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:100249400-100257000	Weak transcription	Fetal Brain Male	brain
18	chr15:100249400-100258600	Strong transcription	Fetal Intestine Large	intestine
19	chr15:100249400-100260200	Weak transcription	A549	lung
20	chr15:100249600-100257200	Strong transcription	Liver	Liver
21	chr15:100249600-100258600	Strong transcription	Primary T cells from cord blood	blood
22	chr15:100249600-100272800	Weak transcription	Small Intestine	intestine
23	chr15:100249800-100272200	Weak transcription	HUVEC	blood vessel
24	chr15:100250800-100256800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:100250800-100257000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:100250800-100257000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:100250800-100258600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:100251800-100261600	Weak transcription	NHEK	skin
29	chr15:100251800-100271800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:100252200-100271400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:100252600-100260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:100253000-100257200	Strong transcription	Fetal Thymus	thymus
33	chr15:100253000-100259800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:100253000-100260800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:100253000-100261000	Weak transcription	Esophagus	oesophagus
36	chr15:100253000-100265000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:100253000-100271800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr15:100253200-100256800	Weak transcription	Ovary	ovary
39	chr15:100253200-100257000	Enhancers	Fetal Heart	heart
40	chr15:100253200-100260800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:100253200-100268400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:100253400-100256800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:100253400-100257000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:100253400-100260200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:100253400-100261400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:100253400-100261400	Weak transcription	Pancreas	Pancrea
47	chr15:100253400-100261400	Weak transcription	HepG2	liver
48	chr15:100253400-100263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:100253600-100256800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:100253600-100256800	Weak transcription	Colon Smooth Muscle	Colon

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