Variant report

Variant	rs8102439
Chromosome Location	chr19:42990382-42990383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10084159	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10401271	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402361	0.82[AMR][1000 genomes]
rs10402677	0.94[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10403517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10404402	0.81[AFR][1000 genomes]
rs10405445	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405646	0.84[AMR][1000 genomes]
rs10405906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407576	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs10412463	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10413413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416089	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10419378	0.83[AMR][1000 genomes]
rs10420796	0.84[AMR][1000 genomes]
rs10421108	0.83[AMR][1000 genomes]
rs10422987	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10423291	0.81[AFR][1000 genomes]
rs10469271	0.84[AMR][1000 genomes]
rs10469284	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469286	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs1076243	0.82[AMR][1000 genomes]
rs11083659	0.83[AMR][1000 genomes]
rs11665870	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11665935	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11666350	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666835	0.84[AMR][1000 genomes]
rs11666862	0.84[AMR][1000 genomes]
rs11668599	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs11671272	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671846	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs11673645	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs11881517	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12611218	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343936	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs16975865	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267631	0.88[CEU][hapmap];0.83[YRI][hapmap]
rs28411988	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4080606	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55850134	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6509016	0.86[AFR][1000 genomes]
rs7248297	0.83[AMR][1000 genomes]
rs7253056	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253209	0.83[AMR][1000 genomes]
rs8102519	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap]
rs8103285	0.94[ASW][hapmap];0.88[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8103891	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8106570	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8107152	0.88[ASW][hapmap];0.88[CEU][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8107254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107790	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8112156	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851302	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9304604	0.82[ASW][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8102439	PTOV1	cis	parietal	SCAN
rs8102439	FTL	cis	cerebellum	SCAN
rs8102439	KLK8	cis	parietal	SCAN
rs8102439	SEC1	cis	cerebellum	SCAN
rs8102439	ZNF223	cis	parietal	SCAN
rs8102439	KCNA7	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42979400-42990800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:42981200-43002000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:42981400-42993000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr19:42985200-42993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:42986000-42990400	Weak transcription	Adipose Nuclei	Adipose
6	chr19:42986000-42999400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr19:42986600-42998200	Weak transcription	Liver	Liver
8	chr19:42987600-42992600	Enhancers	HepG2	liver
9	chr19:42989400-42994000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr19:42989600-42992600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:42989800-42993000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr19:42990000-42991000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:42990200-42990600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:42990200-42992400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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