Variant report

Variant	rs1889918
Chromosome Location	chr10:89834899-89834900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12247999	0.90[JPT][hapmap]
rs17108235	0.91[EUR][1000 genomes]
rs41432945	0.88[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61854363	0.90[EUR][1000 genomes]
rs61854364	0.90[EUR][1000 genomes]
rs61854366	0.90[EUR][1000 genomes]
rs61854367	0.87[EUR][1000 genomes]
rs61854370	0.91[EUR][1000 genomes]
rs61854371	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1042027	chr10:89822721-89851993	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1889918	PCGF5	cis	cerebellum	SCAN
rs1889918	LIPA	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89823000-89835600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr10:89825200-89835000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:89826400-89839200	Weak transcription	Fetal Lung	lung
4	chr10:89826600-89835800	Weak transcription	Psoas Muscle	Psoas
5	chr10:89828200-89839400	Weak transcription	Left Ventricle	heart
6	chr10:89829600-89835600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr10:89830400-89835600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:89830400-89835800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr10:89830400-89838600	Weak transcription	NHLF	lung
10	chr10:89831000-89836000	Weak transcription	Liver	Liver
11	chr10:89831000-89839000	Weak transcription	Lung	lung
12	chr10:89832200-89835000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:89832200-89835600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr10:89832200-89836200	Weak transcription	Spleen	Spleen
15	chr10:89832200-89849600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:89832400-89835400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:89832400-89835600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr10:89832400-89835600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr10:89832400-89835800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr10:89832400-89838400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:89832400-89842600	Weak transcription	Dnd41	blood
22	chr10:89832800-89835400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr10:89833000-89836000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr10:89834400-89835800	Weak transcription	Pancreas	Pancrea
25	chr10:89834800-89835000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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