Variant report

Variant	rs1457144
Chromosome Location	chr19:42338767-42338768
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42337138..42340110-chr19:42342013..42344959,2	MCF-7	breast:
2	chr19:42337957..42339654-chr19:42347181..42349123,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYPD4-1	chr19:42337740-42340005	ENSG00000267839.1

Variant related genes	Relation type
ENSG00000183103	Chromatin interaction
ENSG00000142025	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10401370	0.81[ASN][1000 genomes]
rs10401528	0.83[ASN][1000 genomes]
rs10401928	0.86[ASN][1000 genomes]
rs10404939	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407206	0.89[ASN][1000 genomes]
rs10407619	0.86[ASN][1000 genomes]
rs10407797	0.86[ASN][1000 genomes]
rs10408367	0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10410918	0.87[ASN][1000 genomes]
rs10414356	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10414823	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10416824	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10417985	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap]
rs10426243	0.81[ASN][1000 genomes]
rs10500284	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12461099	0.82[ASN][1000 genomes]
rs12461131	0.82[ASN][1000 genomes]
rs12971550	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12976571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979253	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12984383	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1366610	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1811564	0.82[ASN][1000 genomes]
rs1870092	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs1870093	0.99[ASN][1000 genomes]
rs2008798	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2008808	0.83[ASN][1000 genomes]
rs2075749	0.82[ASN][1000 genomes]
rs2075750	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2075752	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2075754	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs2199829	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2199830	0.87[ASN][1000 genomes]
rs2290695	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305809	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]
rs28821622	0.88[ASN][1000 genomes]
rs28824227	0.93[ASN][1000 genomes]
rs3786536	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3786538	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3795022	0.85[ASN][1000 genomes]
rs3810153	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs3922888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4130852	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4480913	0.85[ASN][1000 genomes]
rs4803511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58857981	0.82[ASN][1000 genomes]
rs6508998	0.87[ASN][1000 genomes]
rs6508999	0.93[ASN][1000 genomes]
rs6509000	0.93[ASN][1000 genomes]
rs6509001	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6509002	0.82[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7248641	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250787	0.82[ASN][1000 genomes]
rs7251336	0.82[CHB][hapmap]
rs7251960	0.82[CHB][hapmap]
rs7252877	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254214	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7257666	0.83[ASN][1000 genomes]
rs7259596	0.82[ASN][1000 genomes]
rs7259967	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs734107	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs73549152	0.82[ASN][1000 genomes]
rs8099934	0.87[ASN][1000 genomes]
rs8100182	0.86[ASN][1000 genomes]
rs8104958	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106505	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8110199	0.87[ASN][1000 genomes]
rs8113283	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs8113538	0.82[ASN][1000 genomes]
rs8113641	0.89[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs8113720	0.82[ASN][1000 genomes]
rs8113741	0.82[ASN][1000 genomes]
rs8113780	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113813	0.82[ASN][1000 genomes]
rs873282	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs882520	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs891167	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs899662	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[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	nsv960847	chr19:42319253-42339596	Enhancers Bivalent Enhancer Weak transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1457144	PSG9	cis	multi-tissue	Pritchard
rs1457144	LIG1	cis	parietal	SCAN
rs1457144	PSG3	cis	multi-tissue	Pritchard
rs1457144	IGFL1	cis	parietal	SCAN
rs1457144	CEACAM1	cis	cerebellum	SCAN
rs1457144	ZNF575	cis	parietal	SCAN
rs1457144	SLC1A5	cis	parietal	SCAN
rs1457144	CEACAM3	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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