Variant report

Variant	rs7253209
Chromosome Location	chr19:43063494-43063495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10084159	0.83[AMR][1000 genomes]
rs10401271	0.84[AMR][1000 genomes]
rs10402361	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402401	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10402677	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10403517	0.88[CEU][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes]
rs10403979	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404402	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10404509	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10405445	0.86[AMR][1000 genomes]
rs10405646	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405906	0.88[ASW][hapmap];0.88[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10407178	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410147	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411165	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411458	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10411945	0.81[EUR][1000 genomes]
rs10412463	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10413014	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs10413413	0.88[CEU][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10414602	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415564	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416089	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10417418	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417693	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419378	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420164	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420796	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421108	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421620	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421881	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10422283	0.82[CHB][hapmap]
rs10422573	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10422987	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10423291	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10425241	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10469271	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469285	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076243	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083659	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665767	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665870	0.88[ASW][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs11665935	0.83[AMR][1000 genomes]
rs11666425	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666835	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666862	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668009	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668460	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669892	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11670316	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671846	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11673645	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11673684	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879306	0.87[ASN][1000 genomes]
rs11881517	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11882150	0.87[ASN][1000 genomes]
rs11882882	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12165114	0.82[CHB][hapmap]
rs12327586	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343936	0.83[AMR][1000 genomes]
rs13346414	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975865	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16975890	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1859341	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28411988	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28447294	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883270	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4499340	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55641435	0.96[ASN][1000 genomes]
rs55850134	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56237547	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56978333	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57902582	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59525393	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60052467	0.84[EUR][1000 genomes]
rs60313903	0.87[ASN][1000 genomes]
rs60662795	0.94[ASN][1000 genomes]
rs6509016	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6509017	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6509020	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247618	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248042	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7248297	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249411	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253056	0.86[AMR][1000 genomes]
rs73562329	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8102439	0.88[ASW][hapmap];0.88[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs8102519	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103285	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103891	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8106083	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106570	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8107152	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8107254	0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs8107790	0.83[AMR][1000 genomes]
rs8108816	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8108844	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs8110766	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110917	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112156	0.86[AMR][1000 genomes]
rs851298	0.87[ASN][1000 genomes]
rs851301	0.87[ASN][1000 genomes]
rs851302	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9304604	0.94[ASW][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
3	esv2422468	chr19:42991289-43669027	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1057390	chr19:43003323-43173028	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv482597	chr19:43037214-43222644	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2758501	chr19:43042747-43899053	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	esv2758763	chr19:43042747-43899053	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv428023	chr19:43042747-43899053	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	esv2422227	chr19:43059426-43669485	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7253209	ETHE1	cis	cerebellum	SCAN
rs7253209	FTL	cis	cerebellum	SCAN
rs7253209	PPP1R13L	cis	parietal	SCAN
rs7253209	PTOV1	cis	parietal	SCAN
rs7253209	KLK8	cis	parietal	SCAN
rs7253209	KCNA7	cis	cerebellum	SCAN
rs7253209	ZNF223	cis	parietal	SCAN
rs7253209	SEC1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43050600-43067800	Weak transcription	Right Atrium	heart
2	chr19:43059800-43064000	Weak transcription	Esophagus	oesophagus
3	chr19:43060200-43064200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr19:43060200-43067600	Weak transcription	Adipose Nuclei	Adipose
5	chr19:43060400-43064200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:43062000-43064200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr19:43062000-43064400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr19:43062000-43064600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr19:43062200-43063800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:43062400-43064800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr19:43062600-43064200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr19:43062600-43064400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr19:43062800-43064400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:43063000-43064000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:43063000-43064000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:43063000-43064000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:43063000-43064600	Enhancers	NHEK	skin
18	chr19:43063200-43063600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:43063200-43064400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:43063400-43063800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:43063400-43063800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:43063400-43063800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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