Variant report

Variant	rs17248670
Chromosome Location	chr19:38319897-38319898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1048505	0.91[ASN][1000 genomes]
rs12150862	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151082	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.91[ASN][1000 genomes]
rs1643455	1.00[CHB][hapmap]
rs1643459	1.00[CHB][hapmap]
rs17248097	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249138	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249336	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs17305823	1.00[JPT][hapmap]
rs17306900	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35153242	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3859549	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614853	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55681348	0.86[ASN][1000 genomes]
rs55743020	0.91[ASN][1000 genomes]
rs55752822	0.81[EUR][1000 genomes]
rs55813548	0.82[EUR][1000 genomes]
rs55974157	0.82[EUR][1000 genomes]
rs55983118	0.81[EUR][1000 genomes]
rs56184201	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56207124	0.81[EUR][1000 genomes]
rs56230664	0.81[EUR][1000 genomes]
rs56233644	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246446	0.81[EUR][1000 genomes]
rs56268127	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56290614	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56351266	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56676595	0.82[EUR][1000 genomes]
rs6508755	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs705501	1.00[CHB][hapmap]
rs7245855	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73027472	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73027480	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73039029	0.91[ASN][1000 genomes]
rs73041006	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73041036	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7343065	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8100199	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8110293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833905	1.00[CHB][hapmap]
rs833919	1.00[CHB][hapmap]
rs833920	1.00[CHB][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs17248670	TRAPPC6A	cis	cerebellum	SCAN
rs17248670	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs17248670	AC012309.5	cis	Muscle Skeletal	GTEx
rs17248670	PLEKHG2	cis	cerebellum	SCAN
rs17248670	AC012309.5	cis	Artery Tibial	GTEx
rs17248670	HKR1	cis	multi-tissue	Pritchard
rs17248670	ZNF781	cis	Thyroid	GTEx
rs17248670	AC012309.5	cis	Thyroid	GTEx
rs17248670	AC012309.5	cis	Esophagus Muscularis	GTEx
rs17248670	PHLDB3	cis	cerebellum	SCAN
rs17248670	AC012309.5	cis	Heart Left Ventricle	GTEx
rs17248670	C19orf61	cis	cerebellum	SCAN
rs17248670	ZNF226	cis	cerebellum	SCAN
rs17248670	ARHGEF1	cis	cerebellum	SCAN
rs17248670	KIAA0961	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38312000-38324000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:38314000-38321600	ZNF genes & repeats	Fetal Lung	lung
3	chr19:38314400-38324600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:38319600-38324800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:38319800-38320000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:38319800-38320200	ZNF genes & repeats	Liver	Liver

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