Variant report

Variant	rs10408367
Chromosome Location	chr19:42309686-42309687
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	chr19:42307703..42310642-chr19:42313204..42315165,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10401370	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10401528	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10401928	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10404939	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10407206	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10407619	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10407797	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10410918	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10414356	0.81[ASN][1000 genomes]
rs10414823	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10416824	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];0.99[ASN][1000 genomes]
rs10417985	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap]
rs10418100	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10419111	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10419827	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10426020	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10426049	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10426243	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10500284	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs12976571	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12979253	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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];0.83[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1811564	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870092	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.98[TSI][hapmap]
rs1870093	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2008798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2008808	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075750	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2075752	0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap]
rs2075754	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2199829	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199830	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290695	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.82[ASN][1000 genomes]
rs2305809	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs28821622	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28824227	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28847113	0.89[EUR][1000 genomes]
rs34819714	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3786536	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3786538	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3795022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4130852	0.81[ASN][1000 genomes]
rs4480913	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803511	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4803512	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs62117403	0.89[EUR][1000 genomes]
rs6508998	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508999	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6509000	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6509002	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7248641	0.82[ASN][1000 genomes]
rs7251154	0.89[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs7251336	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251783	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7251799	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7251960	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7254214	0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.84[MKK][hapmap]
rs7258053	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7259967	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs734107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.97[ASN][1000 genomes]
rs734109	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8099934	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8100182	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8104958	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs8106505	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8110199	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8113283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113538	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113720	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113741	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113780	0.82[ASN][1000 genomes]
rs8113813	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3351362	chr19:42307636-42311347	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10408367	ZNF473	cis	cerebellum	SCAN
rs10408367	PTGIR	cis	parietal	SCAN
rs10408367	CEACAM3	cis	multi-tissue	Pritchard
rs10408367	EXOC3L2	cis	cerebellum	SCAN
rs10408367	PPP5C	cis	parietal	SCAN
rs10408367	CEACAM1	cis	cerebellum	SCAN
rs10408367	ZNF575	cis	parietal	SCAN
rs10408367	DMRTC2	cis	Whole Blood	GTEx
rs10408367	EHD2	cis	parietal	SCAN
rs10408367	PSG9	cis	multi-tissue	Pritchard
rs10408367	PSG3	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42304800-42316800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:42305000-42310000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr19:42307000-42313600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:42307000-42314600	Weak transcription	Fetal Thymus	thymus
5	chr19:42307200-42310000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr19:42307800-42310200	Enhancers	Primary B cells from cord blood	blood
7	chr19:42308800-42310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:42308800-42313000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr19:42308800-42314400	Weak transcription	GM12878-XiMat	blood
10	chr19:42309000-42312000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:42309200-42312200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:42309600-42310600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood

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