Variant report

Variant	rs2540525
Chromosome Location	chr13:51254712-51254713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11617990	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12853149	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1641299	0.80[EUR][1000 genomes]
rs17396905	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17396919	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71436234	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71436235	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71436236	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71436237	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs797538	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription 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	1256 gene(s)	inside rSNPs	diseases
2	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753864	chr13:51136699-51375199	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2540525	RCBTB1	cis	parietal	SCAN
rs2540525	CYSLTR2	cis	parietal	SCAN
rs2540525	CDADC1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51244800-51258200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr13:51247400-51260200	Weak transcription	HepG2	liver
3	chr13:51250000-51255200	Enhancers	Osteobl	bone
4	chr13:51250000-51256200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:51250400-51258400	Weak transcription	Psoas Muscle	Psoas
6	chr13:51250600-51254800	Enhancers	Fetal Heart	heart
7	chr13:51251400-51261000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr13:51251400-51265600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:51252800-51256800	Weak transcription	Dnd41	blood
10	chr13:51252800-51257800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr13:51253000-51256400	Weak transcription	Brain Angular Gyrus	brain
12	chr13:51253000-51257000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr13:51253000-51258400	Weak transcription	Brain Germinal Matrix	brain
14	chr13:51253000-51258400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr13:51253200-51255000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:51253200-51256600	Enhancers	Brain Hippocampus Middle	brain
17	chr13:51253400-51255000	Enhancers	Brain Anterior Caudate	brain
18	chr13:51253400-51255200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:51253400-51256200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:51253400-51256200	Weak transcription	Thymus	Thymus
21	chr13:51253400-51256400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr13:51253400-51256600	Weak transcription	Fetal Muscle Leg	muscle
23	chr13:51253400-51257800	Weak transcription	Left Ventricle	heart
24	chr13:51253400-51258200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr13:51253400-51258200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:51253400-51258400	Weak transcription	Right Atrium	heart
27	chr13:51253400-51259200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:51253400-51265000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:51253600-51256200	Weak transcription	Fetal Thymus	thymus
30	chr13:51253800-51254800	Weak transcription	Brain Substantia Nigra	brain
31	chr13:51254000-51259000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:51254400-51255600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr13:51254400-51257000	Weak transcription	HUVEC	blood vessel
34	chr13:51254400-51259600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr13:51254400-51267800	Weak transcription	Muscle Satellite Cultured Cells	--

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