Variant report

Variant	rs10401928
Chromosome Location	chr19:42317651-42317652
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42294869..42297098-chr19:42316769..42318454,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10401370	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10401528	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10404939	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10407206	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10407619	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407797	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10408367	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10410918	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10414356	0.85[ASN][1000 genomes]
rs10414823	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10416824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10417985	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10418100	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10419111	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419827	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10426020	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10426049	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10426243	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10500284	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12976571	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12979253	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12984383	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1366610	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1457144	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1811564	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1870092	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap]
rs1870093	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2008798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008808	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075750	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2075752	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2075754	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2199829	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199830	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290695	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2305809	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs28821622	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28824227	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28847113	0.89[EUR][1000 genomes]
rs34819714	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3786536	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3786538	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3795022	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810153	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3922888	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4130852	0.85[ASN][1000 genomes]
rs4480913	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803511	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4803512	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.82[ASN][1000 genomes]
rs62117403	0.89[EUR][1000 genomes]
rs6508998	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508999	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6509000	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6509001	0.84[ASN][1000 genomes]
rs6509002	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7248641	0.86[ASN][1000 genomes]
rs7251154	0.89[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs7251336	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251783	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251799	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251960	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7252877	0.81[ASN][1000 genomes]
rs7254214	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7258053	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7259967	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs734107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs734109	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8099934	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100182	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104958	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs8106505	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8110199	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113538	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113720	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113741	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113780	0.86[ASN][1000 genomes]
rs8113813	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873282	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs882520	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs891167	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs899662	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10401928	PSG3	cis	multi-tissue	Pritchard
rs10401928	CCDC9	cis	parietal	SCAN
rs10401928	LIG1	cis	parietal	SCAN
rs10401928	PSG9	cis	multi-tissue	Pritchard
rs10401928	CEACAM3	cis	multi-tissue	Pritchard
rs10401928	EXOC3L2	cis	cerebellum	SCAN
rs10401928	ZNF575	cis	parietal	SCAN
rs10401928	EHD2	cis	parietal	SCAN
rs10401928	CEACAM1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42310600-42317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:42316000-42318800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:42316200-42318200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:42316400-42318600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:42316600-42318600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:42317200-42319000	Enhancers	Primary neutrophils fromperipheralblood	blood

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