Variant report

Variant	rs538292
Chromosome Location	chr10:89925671-89925672
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	chr10:89923474..89925922-chr10:89936717..89938550,2	MCF-7	breast:
2	chr10:89919575..89922469-chr10:89924510..89926380,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs481840	0.90[EUR][1000 genomes]
rs490265	0.87[EUR][1000 genomes]
rs501751	0.87[EUR][1000 genomes]
rs505384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510727	0.87[EUR][1000 genomes]
rs539299	0.90[EUR][1000 genomes]
rs575865	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs577880	0.92[CEU][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs640906	0.90[EUR][1000 genomes]
rs642864	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs538292	LRIT2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89915200-89929600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:89918200-89937600	Weak transcription	Aorta	Aorta
3	chr10:89921600-89927000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:89922000-89937600	Weak transcription	Thymus	Thymus
5	chr10:89923200-89926600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:89923400-89927000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:89923600-89927200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:89924200-89927200	Enhancers	NHDF-Ad	bronchial
9	chr10:89924200-89927400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr10:89924200-89927400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:89924400-89926400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr10:89924600-89927200	Enhancers	Brain Hippocampus Middle	brain
13	chr10:89925000-89926400	Enhancers	Brain Cingulate Gyrus	brain
14	chr10:89925000-89926400	Enhancers	NHLF	lung
15	chr10:89925000-89926600	Enhancers	HMEC	breast
16	chr10:89925000-89927200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:89925200-89926200	Enhancers	Brain Germinal Matrix	brain
18	chr10:89925200-89926400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:89925200-89926600	Enhancers	NH-A	brain
20	chr10:89925200-89927600	Enhancers	Fetal Heart	heart
21	chr10:89925400-89926000	Active TSS	Brain Anterior Caudate	brain
22	chr10:89925400-89926400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr10:89925400-89927400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:89925600-89926000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr10:89925600-89926000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr10:89925600-89926000	Enhancers	Brain Angular Gyrus	brain
27	chr10:89925600-89926000	Active TSS	Brain Substantia Nigra	brain
28	chr10:89925600-89926200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:89925600-89926400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:89925600-89926400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr10:89925600-89926400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr10:89925600-89926400	Enhancers	HSMM	muscle
33	chr10:89925600-89926400	Enhancers	HSMMtube	muscle
34	chr10:89925600-89926400	Enhancers	HUVEC	blood vessel
35	chr10:89925600-89926400	Enhancers	NHEK	skin
36	chr10:89925600-89926400	Enhancers	Osteobl	bone
37	chr10:89925600-89927200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:89925600-89927200	Enhancers	Primary hematopoietic stem cells	blood

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