Variant report

Variant	rs2305809
Chromosome Location	chr19:42354629-42354630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42351673..42358248-chr19:42360570..42366998,12	K562	blood:
2	chr19:42346423..42349202-chr19:42351468..42355829,7	K562	blood:
3	chr19:42354421..42356282-chr19:42374725..42377333,2	MCF-7	breast:
4	chr19:42349297..42351967-chr19:42352906..42355134,2	K562	blood:
5	chr19:42346706..42349091-chr19:42352503..42356782,5	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS19-1	chr19:42354312-42354768	NONHSAT066493

No data

Variant related genes	Relation type
ENSG00000105372	Chromatin interaction
ENSG00000183103	Chromatin interaction
ENSG00000142025	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10401528	0.80[ASN][1000 genomes]
rs10401928	0.84[ASN][1000 genomes]
rs10404939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10407206	0.86[ASN][1000 genomes]
rs10407619	0.84[ASN][1000 genomes]
rs10407797	0.83[ASN][1000 genomes]
rs10408367	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs10410918	0.84[ASN][1000 genomes]
rs10414356	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10414823	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10416824	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10417985	0.90[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10500284	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12461099	0.85[ASN][1000 genomes]
rs12461131	0.85[ASN][1000 genomes]
rs12971550	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12976571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12979253	0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12984383	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1366610	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1457144	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1870092	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs1870093	0.96[ASN][1000 genomes]
rs2008798	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2008808	0.81[ASN][1000 genomes]
rs2075749	0.84[ASN][1000 genomes]
rs2075750	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2075752	0.90[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2075754	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2199829	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2199830	0.84[ASN][1000 genomes]
rs2290695	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28821622	0.85[ASN][1000 genomes]
rs28824227	0.90[ASN][1000 genomes]
rs3786536	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3786538	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3795022	0.82[ASN][1000 genomes]
rs3810153	0.95[CHB][hapmap]
rs3922888	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4130852	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4480913	0.82[ASN][1000 genomes]
rs4803511	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803512	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58857981	0.84[ASN][1000 genomes]
rs6508998	0.84[ASN][1000 genomes]
rs6508999	0.90[ASN][1000 genomes]
rs6509000	0.90[ASN][1000 genomes]
rs6509001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509002	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248641	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250787	0.84[ASN][1000 genomes]
rs7251336	0.82[CHB][hapmap];0.82[LWK][hapmap]
rs7251960	0.82[CHB][hapmap]
rs7252877	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254214	0.80[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7257666	0.86[ASN][1000 genomes]
rs7258163	0.80[ASN][1000 genomes]
rs7259596	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7259967	1.00[CHB][hapmap]
rs734107	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs73549152	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7408605	0.80[MKK][hapmap]
rs8099934	0.84[ASN][1000 genomes]
rs8100182	0.84[ASN][1000 genomes]
rs8102670	0.81[ASN][1000 genomes]
rs8104958	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106505	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs8110199	0.84[ASN][1000 genomes]
rs8113283	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs8113641	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs8113780	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs873282	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs882520	0.95[CHB][hapmap]
rs891167	0.83[CHB][hapmap]
rs899662	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs930102	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2305809	ZNF575	cis	parietal	SCAN
rs2305809	LIG1	cis	parietal	SCAN
rs2305809	IGFL1	cis	parietal	SCAN
rs2305809	SLC1A5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42352000-42363800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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