Variant report

Variant	rs4520717
Chromosome Location	chr13:40103151-40103152
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PROSER1-3	chr13:40100016-40107556	NONHSAT033305

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1022808	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1570414	0.94[CEU][hapmap]
rs1570417	0.95[ASN][1000 genomes]
rs1885758	1.00[CEU][hapmap]
rs1885760	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1885762	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2324344	0.81[JPT][hapmap]
rs2324345	0.81[JPT][hapmap]
rs2875329	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4142372	0.81[JPT][hapmap]
rs4325425	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4941933	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4941934	0.88[ASN][1000 genomes]
rs4941935	0.85[EUR][1000 genomes]
rs4943674	0.86[EUR][1000 genomes]
rs6563719	0.82[CEU][hapmap]
rs6563720	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6563721	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6563726	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6563727	1.00[CEU][hapmap]
rs7324883	1.00[CEU][hapmap]
rs7331023	1.00[CEU][hapmap]
rs7333587	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7986879	1.00[ASN][1000 genomes]
rs7988729	1.00[CEU][hapmap]
rs912050	1.00[CEU][hapmap]
rs9285135	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9285136	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9315698	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9315704	1.00[CEU][hapmap]
rs9315705	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9532393	1.00[ASN][1000 genomes]
rs9548796	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9548807	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9566448	0.87[CEU][hapmap];0.90[AMR][1000 genomes]
rs9566457	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576865	1.00[CEU][hapmap]
rs9576869	0.81[JPT][hapmap]
rs978135	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1050137	chr13:40090742-40118499	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40096800-40110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:40099400-40106000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:40100600-40103400	Enhancers	Fetal Heart	heart
4	chr13:40100600-40103600	Enhancers	Left Ventricle	heart
5	chr13:40101000-40103200	Enhancers	Brain Substantia Nigra	brain
6	chr13:40101200-40103200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:40101200-40103200	Enhancers	HMEC	breast
8	chr13:40101400-40103200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:40101400-40103200	Enhancers	HUVEC	blood vessel
10	chr13:40101400-40103400	Enhancers	Fetal Muscle Leg	muscle
11	chr13:40101600-40105000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:40101600-40110400	Weak transcription	Psoas Muscle	Psoas
13	chr13:40102000-40103200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr13:40102200-40103200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr13:40102200-40103200	Enhancers	Adipose Nuclei	Adipose
16	chr13:40102200-40103200	Enhancers	Fetal Brain Female	brain
17	chr13:40102400-40103200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:40102400-40103200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:40102400-40103400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:40102600-40103200	Enhancers	NHEK	skin
21	chr13:40102600-40105000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr13:40102600-40110600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr13:40102800-40103200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:40102800-40103200	Enhancers	A549	lung
25	chr13:40102800-40103200	Enhancers	HSMMtube	muscle
26	chr13:40102800-40103400	Enhancers	HSMM	muscle
27	chr13:40102800-40103400	Enhancers	NH-A	brain
28	chr13:40102800-40103400	Enhancers	NHLF	lung
29	chr13:40102800-40103600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr13:40102800-40103600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr13:40102800-40103800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:40102800-40104200	Weak transcription	Right Ventricle	heart
33	chr13:40102800-40104200	Enhancers	Osteobl	bone
34	chr13:40102800-40104400	Weak transcription	Right Atrium	heart
35	chr13:40102800-40104800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:40102800-40104800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr13:40102800-40104800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr13:40102800-40105000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr13:40102800-40105000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr13:40102800-40105000	Weak transcription	Colon Smooth Muscle	Colon
41	chr13:40102800-40105000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr13:40102800-40106000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr13:40102800-40106400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr13:40102800-40107600	Weak transcription	Ovary	ovary
45	chr13:40102800-40107800	Weak transcription	Fetal Brain Male	brain
46	chr13:40102800-40110400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr13:40102800-40110800	Weak transcription	Brain Hippocampus Middle	brain
48	chr13:40102800-40111200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr13:40103000-40103400	Enhancers	Fetal Lung	lung
50	chr13:40103000-40104400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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