Variant report

Variant	rs497240
Chromosome Location	chr6:69542291-69542292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:69539780..69542315-chr6:69542926..69545081,3	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10485433	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10806607	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10945147	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs1120509	0.89[ASN][1000 genomes]
rs12055424	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12174093	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12191891	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs13193787	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs1403926	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523938	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1932611	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1932616	0.91[CHD][hapmap];0.95[JPT][hapmap]
rs1932617	0.95[JPT][hapmap]
rs2224011	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2224014	0.89[ASN][1000 genomes]
rs2342760	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2342763	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs28594921	0.89[ASN][1000 genomes]
rs3798966	0.82[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs3798967	0.82[CHB][hapmap]
rs3823059	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4706061	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4706710	0.81[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[ASN][1000 genomes]
rs4706712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472367	0.90[ASN][1000 genomes]
rs478789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480816	0.89[ASN][1000 genomes]
rs482005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs482872	0.89[ASN][1000 genomes]
rs483875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs484684	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs484750	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs485721	0.86[ASN][1000 genomes]
rs486413	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs487408	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs487492	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs489218	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491833	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491928	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs492229	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs492823	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs492831	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs492954	0.93[ASN][1000 genomes]
rs493682	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs493768	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496481	0.89[ASN][1000 genomes]
rs497728	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs499251	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs500125	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs501140	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs501856	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504160	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs505369	0.85[ASN][1000 genomes]
rs505948	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs506211	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs507326	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs508920	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs509304	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs509984	0.90[ASN][1000 genomes]
rs510779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512094	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs512476	0.89[ASN][1000 genomes]
rs513369	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs514518	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs514545	0.89[ASN][1000 genomes]
rs522513	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs523962	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs525342	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs527932	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528718	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs529105	0.89[ASN][1000 genomes]
rs530244	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs533890	0.89[ASN][1000 genomes]
rs534690	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs536054	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs536322	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs538973	0.88[ASN][1000 genomes]
rs539111	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs540955	0.89[ASN][1000 genomes]
rs540974	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541027	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs542600	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs542737	0.89[ASN][1000 genomes]
rs544398	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs547423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs550348	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550695	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs551216	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs551876	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs552283	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs553117	0.89[ASN][1000 genomes]
rs553613	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555588	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs555959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558452	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs562537	0.81[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[ASN][1000 genomes]
rs563146	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs563817	0.89[ASN][1000 genomes]
rs564048	0.89[ASN][1000 genomes]
rs565292	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs566537	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs568360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570276	0.89[ASN][1000 genomes]
rs570379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573776	0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs577328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577894	0.89[ASN][1000 genomes]
rs579304	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs579588	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs579773	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs580182	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs580973	0.90[ASN][1000 genomes]
rs590889	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6906092	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6912997	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6920573	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6927848	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6937418	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6941602	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7747549	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs9342736	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9346252	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9346257	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9351741	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9363974	0.87[ASN][1000 genomes]
rs9446070	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9454636	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454639	0.92[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs951399	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9689807	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][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	nsv886131	chr6:69480628-69545903	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv886132	chr6:69487204-69610281	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs497240	COL19A1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69532800-69548000	Weak transcription	Fetal Lung	lung
2	chr6:69536800-69547800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:69537000-69545000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:69537000-69545800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:69541800-69544400	Weak transcription	K562	blood

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