Variant report

Variant	rs41432945
Chromosome Location	chr10:89831554-89831555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89829976..89832941-chr19:14529125..14530950,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123136	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17108235	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108242	0.88[ASN][1000 genomes]
rs17108289	0.85[ASN][1000 genomes]
rs1889918	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56174856	0.81[ASN][1000 genomes]
rs61854363	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854364	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854366	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854367	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854370	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854371	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854375	0.81[ASN][1000 genomes]
rs61854436	0.81[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41432945	PCGF5	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89819800-89832800	Enhancers	Primary B cells from peripheral blood	blood
2	chr10:89820800-89832400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr10:89823000-89835600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:89825200-89831600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:89825200-89835000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr10:89826400-89839200	Weak transcription	Fetal Lung	lung
7	chr10:89826600-89831600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:89826600-89835800	Weak transcription	Psoas Muscle	Psoas
9	chr10:89827200-89831600	Weak transcription	Fetal Muscle Leg	muscle
10	chr10:89828200-89831600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr10:89828200-89831600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:89828200-89839400	Weak transcription	Left Ventricle	heart
13	chr10:89828400-89832000	Weak transcription	Thymus	Thymus
14	chr10:89829400-89831600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr10:89829400-89832200	Enhancers	NHDF-Ad	bronchial
16	chr10:89829600-89831600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr10:89829600-89831600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr10:89829600-89831800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:89829600-89835600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr10:89830000-89832200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr10:89830200-89831800	Weak transcription	Spleen	Spleen
22	chr10:89830200-89832000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:89830400-89832400	Enhancers	Primary B cells from cord blood	blood
24	chr10:89830400-89835600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:89830400-89835800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:89830400-89838600	Weak transcription	NHLF	lung
27	chr10:89830800-89832400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr10:89830800-89832400	Enhancers	Primary hematopoietic stem cells	blood
29	chr10:89830800-89832400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr10:89830800-89832400	Enhancers	GM12878-XiMat	blood
31	chr10:89830800-89833200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:89831000-89836000	Weak transcription	Liver	Liver
33	chr10:89831000-89839000	Weak transcription	Lung	lung
34	chr10:89831200-89832000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr10:89831200-89832400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr10:89831200-89832400	Enhancers	Fetal Thymus	thymus
37	chr10:89831400-89832200	Enhancers	Primary T cells from cord blood	blood
38	chr10:89831400-89832200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr10:89831400-89832200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:89831400-89832400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:89831400-89832400	Enhancers	Dnd41	blood

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