Variant report

Variant	rs575865
Chromosome Location	chr10:89919005-89919006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTEN-8	chr10:89917585-89919220	NONHSAT015469

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs481840	0.81[EUR][1000 genomes]
rs505384	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs538292	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs539299	0.81[EUR][1000 genomes]
rs577880	0.91[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs640906	0.81[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	esv3329942	chr10:89918572-89920520	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs575865	LRIT2	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89909200-89919200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:89909200-89919200	Enhancers	NHDF-Ad	bronchial
3	chr10:89909400-89919200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr10:89912800-89925000	Weak transcription	Left Ventricle	heart
5	chr10:89913000-89924400	Weak transcription	Right Atrium	heart
6	chr10:89914000-89919200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:89915200-89929600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:89915800-89919200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr10:89915800-89919200	Enhancers	HSMM	muscle
10	chr10:89915800-89919200	Enhancers	HUVEC	blood vessel
11	chr10:89915800-89919200	Enhancers	NH-A	brain
12	chr10:89916000-89919200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:89916000-89919200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:89916000-89919200	Enhancers	HMEC	breast
15	chr10:89916200-89919200	Enhancers	NHEK	skin
16	chr10:89916600-89919800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:89917200-89919200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr10:89917200-89919200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:89917200-89919200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:89917200-89919200	Enhancers	Fetal Stomach	stomach
21	chr10:89917200-89919200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr10:89917400-89919200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:89917400-89919200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:89917400-89919200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr10:89917400-89919200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr10:89917400-89919200	Enhancers	Fetal Lung	lung
27	chr10:89917400-89919200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr10:89917600-89919200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr10:89918000-89919200	Enhancers	Small Intestine	intestine
30	chr10:89918200-89920400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:89918200-89937600	Weak transcription	Aorta	Aorta
32	chr10:89918400-89922200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr10:89918400-89925600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr10:89918600-89919200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:89918600-89919200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr10:89918600-89919200	Flanking Active TSS	Hela-S3	cervix
37	chr10:89918600-89919200	Enhancers	NHLF	lung
38	chr10:89918800-89919200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:89918800-89919200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr10:89918800-89919200	Enhancers	Ovary	ovary
41	chr10:89918800-89919200	Enhancers	Psoas Muscle	Psoas
42	chr10:89918800-89919200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr10:89918800-89919200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr10:89918800-89919200	Flanking Active TSS	Osteobl	bone
45	chr10:89919000-89919200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:89919000-89919200	Enhancers	Dnd41	blood
47	chr10:89919000-89924200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links