Variant report

Variant	rs2686779
Chromosome Location	chr19:44973969-44973970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10221512	0.83[ASN][1000 genomes]
rs17727484	0.94[ASN][1000 genomes]
rs1996823	0.82[GIH][hapmap]
rs2020083	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2253210	0.82[GIH][hapmap]
rs2293164	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2571042	0.82[GIH][hapmap]
rs2571043	0.82[GIH][hapmap]
rs2571051	0.82[GIH][hapmap]
rs2571056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2571108	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs2722702	0.84[CHD][hapmap]
rs3745146	0.81[ASN][1000 genomes]
rs3745147	0.81[ASN][1000 genomes]
rs4141695	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs45562836	0.99[ASN][1000 genomes]
rs566838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57946353	0.86[ASN][1000 genomes]
rs60625660	0.91[ASN][1000 genomes]
rs612890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954313	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv524201	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv525472	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv912115	chr19:44957508-44995990	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv960853	chr19:44958445-44982821	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv978867	chr19:44963452-44982821	ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2686779	GRWD1	cis	cerebellum	SCAN
rs2686779	KLK3	cis	cerebellum	SCAN
rs2686779	PGLYRP1	cis	parietal	SCAN
rs2686779	KDELR1	cis	cerebellum	SCAN
rs2686779	RTN2	cis	cerebellum	SCAN
rs2686779	ZNF180	cis	Muscle Skeletal	GTEx
rs2686779	PTOV1	cis	cerebellum	SCAN
rs2686779	ZNF432	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44966800-44992400	ZNF genes & repeats	Liver	Liver
2	chr19:44967200-44992800	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:44969800-44992200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:44971600-44992200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:44972200-44974600	ZNF genes & repeats	Brain Hippocampus Middle	brain
6	chr19:44972400-44977600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:44972600-44992200	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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