Variant report

Variant	rs10407619
Chromosome Location	chr19:42317872-42317873
allele	A/G
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: 8 )

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

rs_ID	r²[population]
rs10401370	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10401528	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10401928	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10407797	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10408367	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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10410918	0.98[AMR][1000 genomes];0.99[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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10416824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10417985	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10418100	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10419111	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419827	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10426020	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10426049	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10426243	0.87[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];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12976571	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12979253	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[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];0.93[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs1457144	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1811564	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1870092	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap]
rs1870093	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2008798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008808	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075750	0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap]
rs2075752	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2075754	0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs2199829	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];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28824227	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28847113	0.90[EUR][1000 genomes]
rs34819714	0.91[AMR][1000 genomes];0.93[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];0.95[LWK][hapmap];0.85[MKK][hapmap];0.94[YRI][hapmap]
rs3795022	0.95[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	0.92[AMR][1000 genomes];0.99[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];0.82[ASN][1000 genomes]
rs62117403	0.90[EUR][1000 genomes]
rs6508998	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508999	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6509000	0.95[AMR][1000 genomes];0.98[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];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7251783	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251799	0.90[AMR][1000 genomes];0.96[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];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7252877	0.81[ASN][1000 genomes]
rs7254214	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7258053	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7259967	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs734107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs734109	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8099934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8110199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113538	0.91[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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113720	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113741	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113780	0.86[ASN][1000 genomes]
rs8113813	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873282	0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.94[YRI][hapmap]
rs882520	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs891167	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs899662	0.96[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];0.95[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10407619	ZNF575	cis	parietal	SCAN
rs10407619	CEACAM1	cis	cerebellum	SCAN
rs10407619	EXOC3L2	cis	cerebellum	SCAN
rs10407619	LIG1	cis	parietal	SCAN
rs10407619	CCDC9	cis	parietal	SCAN
rs10407619	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs10407619	EHD2	cis	parietal	SCAN
rs10407619	DMRTC2	cis	Whole Blood	GTEx

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

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

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