Variant report

Variant	rs2722737
Chromosome Location	chr19:44852134-44852135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1233428	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1233441	0.83[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs1233444	0.83[CEU][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs1233447	0.84[ASN][1000 genomes]
rs1233448	0.84[ASN][1000 genomes]
rs1233459	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1233466	0.84[ASN][1000 genomes]
rs1233467	0.84[ASN][1000 genomes]
rs1233468	0.82[ASN][1000 genomes]
rs1233470	0.83[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12974099	0.94[ASN][1000 genomes]
rs1434574	0.99[ASN][1000 genomes]
rs1582	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1808735	0.96[ASN][1000 genomes]
rs1821458	0.96[ASN][1000 genomes]
rs1821459	0.96[ASN][1000 genomes]
rs2571062	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571063	0.90[AFR][1000 genomes]
rs2571065	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2571099	1.00[ASN][1000 genomes]
rs2571101	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2571102	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571104	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2609874	0.82[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2609875	0.83[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609877	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609880	0.96[ASN][1000 genomes]
rs2609894	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609895	0.94[ASN][1000 genomes]
rs2609896	0.94[ASN][1000 genomes]
rs2609897	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609908	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2722714	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2722720	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2722722	0.96[ASN][1000 genomes]
rs2722723	0.96[ASN][1000 genomes]
rs2722725	0.96[ASN][1000 genomes]
rs2722726	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2722727	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2722731	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2722740	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2722751	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4280359	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4325673	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4640292	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7249559	0.94[ASN][1000 genomes]
rs892595	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912110	chr19:44840789-44902190	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv963093	chr19:44850276-44876742	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv912111	chr19:44852134-44902190	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv579855	chr19:44852134-44930348	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv515911	chr19:44852134-44935019	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2722737	PTOV1	cis	cerebellum	SCAN
rs2722737	PRRG2	cis	cerebellum	SCAN
rs2722737	HAS1	cis	parietal	SCAN
rs2722737	FPR3	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44823200-44856200	ZNF genes & repeats	Liver	Liver
2	chr19:44840800-44860000	Weak transcription	NHDF-Ad	bronchial
3	chr19:44844200-44859600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:44844200-44859800	Weak transcription	Osteobl	bone
5	chr19:44844800-44853000	Weak transcription	HSMMtube	muscle
6	chr19:44845000-44860000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:44845200-44860000	Weak transcription	HSMM	muscle
8	chr19:44845400-44859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:44847000-44853200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:44847400-44855200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr19:44847800-44855400	Weak transcription	Right Ventricle	heart
12	chr19:44848200-44852200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:44848200-44853400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:44848200-44854800	Weak transcription	Fetal Brain Male	brain
15	chr19:44849000-44852200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:44849000-44852800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:44849600-44859800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:44850000-44853400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:44850400-44860000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:44850400-44860200	Weak transcription	Left Ventricle	heart
21	chr19:44851400-44860400	Weak transcription	Aorta	Aorta
22	chr19:44851600-44852600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:44852000-44853600	ZNF genes & repeats	A549	lung

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