Variant report

Variant	rs1885763
Chromosome Location	chr13:40101329-40101330
allele	A/T
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: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1022808	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs1022810	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1570417	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1885758	0.82[CEU][hapmap]
rs1885761	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885764	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2875329	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3812881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4325425	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6563720	0.82[CEU][hapmap]
rs6563721	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6563722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7139592	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7331023	0.82[CEU][hapmap]
rs7992290	0.94[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9285135	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9285136	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9315698	1.00[ASN][1000 genomes]
rs9315704	0.82[CEU][hapmap]
rs9532387	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9548796	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs9576865	0.82[CEU][hapmap]

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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40077600-40101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40090600-40102400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr13:40090800-40102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:40096200-40101600	Weak transcription	Brain Angular Gyrus	brain
5	chr13:40096600-40101400	Weak transcription	Aorta	Aorta
6	chr13:40096800-40101400	Weak transcription	Right Atrium	heart
7	chr13:40096800-40102000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr13:40096800-40110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:40098800-40102000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:40098800-40102400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:40099000-40101400	Weak transcription	NHEK	skin
12	chr13:40099000-40102400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:40099400-40102200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:40099400-40102200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr13:40099400-40102200	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:40099400-40106000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:40099600-40102000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:40099600-40102400	Enhancers	Osteobl	bone
19	chr13:40099800-40103000	Weak transcription	Fetal Lung	lung
20	chr13:40100200-40102200	Enhancers	NHDF-Ad	bronchial
21	chr13:40100200-40102400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr13:40100600-40101600	Enhancers	Psoas Muscle	Psoas
23	chr13:40100600-40102400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:40100600-40102800	Enhancers	Ovary	ovary
25	chr13:40100600-40103400	Enhancers	Fetal Heart	heart
26	chr13:40100600-40103600	Enhancers	Left Ventricle	heart
27	chr13:40100800-40101600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:40100800-40101600	Enhancers	Right Ventricle	heart
29	chr13:40100800-40102200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr13:40100800-40102200	Enhancers	NHLF	lung
31	chr13:40100800-40102400	Enhancers	NH-A	brain
32	chr13:40101000-40102400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr13:40101000-40103200	Enhancers	Brain Substantia Nigra	brain
34	chr13:40101200-40101600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:40101200-40102200	Enhancers	A549	lung
36	chr13:40101200-40102400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:40101200-40102400	Enhancers	HSMM	muscle
38	chr13:40101200-40103200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:40101200-40103200	Enhancers	HMEC	breast

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