Variant report

Variant	rs2722738
Chromosome Location	chr19:44855757-44855758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1233430	0.82[MEX][hapmap]
rs1233434	0.82[MEX][hapmap]
rs1347349	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1369100	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1836273	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164112	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2164113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2168990	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2196185	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2249402	0.89[ASN][1000 genomes]
rs2262860	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446491	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2466421	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2571100	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2571105	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2571106	0.90[ASN][1000 genomes]
rs2609881	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2609883	0.89[ASN][1000 genomes]
rs2609887	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2609889	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2609890	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2609892	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2609898	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609905	0.85[ASN][1000 genomes]
rs2609906	0.89[ASN][1000 genomes]
rs2609907	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs2722707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2722708	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2722711	0.89[ASN][1000 genomes]
rs2722715	0.89[ASN][1000 genomes]
rs2722716	0.89[ASN][1000 genomes]
rs2722717	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2722718	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2722719	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2722721	0.96[CHD][hapmap];0.96[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2722735	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722736	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722739	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59555311	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6509153	0.89[ASN][1000 genomes]
rs874187	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs898175	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs898176	0.89[ASN][1000 genomes]
rs898177	0.89[ASN][1000 genomes]
rs898179	0.87[ASN][1000 genomes]
rs984116	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv579856	chr19:44855757-44899820	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2722738	SAE1	cis	parietal	SCAN
rs2722738	GLTSCR1	cis	cerebellum	SCAN
rs2722738	ZFP112	trans	cerebellum	SCAN
rs2722738	BAX	cis	cerebellum	SCAN
rs2722738	LIG1	cis	cerebellum	SCAN
rs2722738	SIGLEC16	cis	cerebellum	SCAN
rs2722738	RPS11	cis	cerebellum	SCAN
rs2722738	ZNF229	trans	cerebellum	SCAN
rs2722738	ZNF473	cis	cerebellum	SCAN
rs2722738	KLC3	cis	parietal	SCAN

Chromatin state (count:19 , 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	chr19:44845000-44860000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:44845200-44860000	Weak transcription	HSMM	muscle
7	chr19:44845400-44859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:44849600-44859800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:44850400-44860000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:44850400-44860200	Weak transcription	Left Ventricle	heart
11	chr19:44851400-44860400	Weak transcription	Aorta	Aorta
12	chr19:44852600-44859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:44854400-44860000	Weak transcription	Ovary	ovary
14	chr19:44854800-44857200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:44854800-44860000	Weak transcription	Pancreas	Pancrea
16	chr19:44855000-44859600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:44855400-44858000	Weak transcription	A549	lung
18	chr19:44855400-44860000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:44855600-44860000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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