Variant report

Variant	rs6563719
Chromosome Location	chr13:40097904-40097905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1022808	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs1022810	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040961	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1570417	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1885758	0.82[CEU][hapmap]
rs1885760	0.81[CEU][hapmap]
rs1885761	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885763	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]
rs1885764	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2875329	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs3812881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325425	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]
rs4520717	0.82[CEU][hapmap]
rs6563720	0.82[CEU][hapmap]
rs6563721	0.99[ASN][1000 genomes]
rs6563722	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6563726	0.82[CEU][hapmap]
rs6563727	0.82[CEU][hapmap]
rs7139592	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324883	0.82[CEU][hapmap]
rs7331023	0.82[CEU][hapmap]
rs7988729	0.82[CEU][hapmap]
rs7992290	0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs912050	0.81[CEU][hapmap]
rs9285135	0.99[ASN][1000 genomes]
rs9285136	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9315698	0.99[ASN][1000 genomes]
rs9315704	0.82[CEU][hapmap]
rs9315705	0.82[CEU][hapmap]
rs9532387	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548796	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs9576865	0.82[CEU][hapmap]
rs978135	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv2761784	chr13:40086325-40100095	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
4	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:22 , 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	chr13:40090600-40100800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr13:40090600-40102400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr13:40090800-40102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:40093800-40100800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr13:40096200-40098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:40096200-40098200	Weak transcription	NHEK	skin
8	chr13:40096200-40099000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:40096200-40099600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:40096200-40101600	Weak transcription	Brain Angular Gyrus	brain
11	chr13:40096600-40101400	Weak transcription	Aorta	Aorta
12	chr13:40096800-40098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr13:40096800-40098800	Weak transcription	Brain Substantia Nigra	brain
14	chr13:40096800-40099200	Weak transcription	Right Ventricle	heart
15	chr13:40096800-40100600	Weak transcription	Ovary	ovary
16	chr13:40096800-40101400	Weak transcription	Right Atrium	heart
17	chr13:40096800-40102000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr13:40096800-40110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr13:40097000-40101200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:40097200-40099600	Weak transcription	Fetal Heart	heart
21	chr13:40097600-40099400	Weak transcription	Left Ventricle	heart
22	chr13:40097800-40099800	Enhancers	Fetal Lung	lung

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