Variant report

Variant	rs4325425
Chromosome Location	chr13:40101913-40101914
allele	C/G/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: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1022808	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1022810	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1040961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1570414	0.92[CEU][hapmap]
rs1885758	1.00[CEU][hapmap]
rs1885760	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1885761	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1885762	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1885763	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]
rs1885764	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2875329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4520717	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4941933	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4941935	0.84[EUR][1000 genomes]
rs4943674	0.85[EUR][1000 genomes]
rs6563719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6563720	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6563721	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6563726	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6563727	1.00[CEU][hapmap]
rs7139592	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7324883	1.00[CEU][hapmap]
rs7331023	1.00[CEU][hapmap]
rs7333587	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7988729	1.00[CEU][hapmap]
rs7992290	0.84[CHB][hapmap]
rs912050	1.00[CEU][hapmap]
rs9285135	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315698	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315704	1.00[CEU][hapmap]
rs9315705	1.00[CEU][hapmap]
rs9548796	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9548807	0.86[EUR][1000 genomes]
rs9566448	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9566457	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9576865	1.00[CEU][hapmap]
rs978135	1.00[CEU][hapmap];0.85[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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40090600-40102400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr13:40090800-40102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:40096800-40102000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr13:40096800-40110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:40098800-40102000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:40098800-40102400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:40099000-40102400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:40099400-40102200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr13:40099400-40102200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr13:40099400-40102200	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:40099400-40106000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:40099600-40102000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:40099600-40102400	Enhancers	Osteobl	bone
14	chr13:40099800-40103000	Weak transcription	Fetal Lung	lung
15	chr13:40100200-40102200	Enhancers	NHDF-Ad	bronchial
16	chr13:40100200-40102400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr13:40100600-40102400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:40100600-40102800	Enhancers	Ovary	ovary
19	chr13:40100600-40103400	Enhancers	Fetal Heart	heart
20	chr13:40100600-40103600	Enhancers	Left Ventricle	heart
21	chr13:40100800-40102200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr13:40100800-40102200	Enhancers	NHLF	lung
23	chr13:40100800-40102400	Enhancers	NH-A	brain
24	chr13:40101000-40102400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:40101000-40103200	Enhancers	Brain Substantia Nigra	brain
26	chr13:40101200-40102200	Enhancers	A549	lung
27	chr13:40101200-40102400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr13:40101200-40102400	Enhancers	HSMM	muscle
29	chr13:40101200-40103200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:40101200-40103200	Enhancers	HMEC	breast
31	chr13:40101400-40102000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:40101400-40102200	Enhancers	NHEK	skin
33	chr13:40101400-40102400	Enhancers	HSMMtube	muscle
34	chr13:40101400-40102800	Enhancers	Fetal Brain Male	brain
35	chr13:40101400-40102800	Enhancers	Right Atrium	heart
36	chr13:40101400-40103000	Enhancers	Placenta Amnion	Placenta Amnion
37	chr13:40101400-40103200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:40101400-40103200	Enhancers	HUVEC	blood vessel
39	chr13:40101400-40103400	Enhancers	Fetal Muscle Leg	muscle
40	chr13:40101600-40102000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:40101600-40102200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:40101600-40102200	Weak transcription	Aorta	Aorta
43	chr13:40101600-40102400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:40101600-40102400	Weak transcription	Right Ventricle	heart
45	chr13:40101600-40102800	Enhancers	Brain Angular Gyrus	brain
46	chr13:40101600-40105000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:40101600-40110400	Weak transcription	Psoas Muscle	Psoas
48	chr13:40101800-40102800	Enhancers	Colon Smooth Muscle	Colon

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