Variant report

Variant	rs10416824
Chromosome Location	chr19:42310388-42310389
allele	C/T
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: 85 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10401370	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10401528	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10401928	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10404939	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10407206	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10407619	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10407797	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[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];0.99[ASN][1000 genomes]
rs10410918	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10414356	0.82[ASN][1000 genomes]
rs10414823	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10417985	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10418100	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419111	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419827	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10426020	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10426049	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10426243	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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];0.81[ASN][1000 genomes]
rs12976571	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[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];0.89[ASN][1000 genomes]
rs12984383	0.90[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap]
rs1366610	0.91[CHB][hapmap];0.83[JPT][hapmap];0.84[LWK][hapmap];0.94[YRI][hapmap]
rs1457144	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1811564	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.84[ASN][1000 genomes]
rs2008798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2008808	0.87[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];0.86[LWK][hapmap];0.94[YRI][hapmap]
rs2075752	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2075754	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.94[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];0.99[ASN][1000 genomes]
rs2199830	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290695	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2305809	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs28821622	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28824227	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28847113	0.90[EUR][1000 genomes]
rs34819714	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3786536	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3786538	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs3795022	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.82[ASN][1000 genomes]
rs4130852	0.82[ASN][1000 genomes]
rs4480913	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803511	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4803512	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs62117403	0.90[EUR][1000 genomes]
rs6508998	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508999	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6509000	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6509001	0.81[ASN][1000 genomes]
rs6509002	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7248641	0.84[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];0.83[ASN][1000 genomes]
rs7251783	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7251799	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[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]
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];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs734109	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8099934	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8100182	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104958	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.84[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];0.90[ASN][1000 genomes]
rs8110199	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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];0.99[ASN][1000 genomes]
rs8113538	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.99[ASN][1000 genomes]
rs8113720	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113741	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8113780	0.84[ASN][1000 genomes]
rs8113813	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs873282	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.89[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: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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10416824	ZNF473	cis	cerebellum	SCAN
rs10416824	PTGIR	cis	parietal	SCAN
rs10416824	PSG3	cis	multi-tissue	Pritchard
rs10416824	PSG9	cis	multi-tissue	Pritchard
rs10416824	EHD2	cis	parietal	SCAN
rs10416824	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs10416824	CEACAM3	cis	multi-tissue	Pritchard
rs10416824	EXOC3L2	cis	cerebellum	SCAN
rs10416824	CEACAM1	cis	cerebellum	SCAN
rs10416824	PPP5C	cis	parietal	SCAN
rs10416824	ZNF575	cis	parietal	SCAN
rs10416824	DMRTC2	cis	Whole Blood	GTEx

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	chr19:42307000-42313600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:42307000-42314600	Weak transcription	Fetal Thymus	thymus
4	chr19:42308800-42313000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:42308800-42314400	Weak transcription	GM12878-XiMat	blood
6	chr19:42309000-42312000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:42309200-42312200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:42309600-42310600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
9	chr19:42310000-42311400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr19:42310000-42312000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:42310200-42311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:42310200-42311800	Weak transcription	Primary B cells from cord blood	blood

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