Variant report

Variant	rs619784
Chromosome Location	chr1:93454314-93454315
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	chr1:93452194..93457760-chr1:93458258..93461631,4	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1011663	0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs10747454	0.82[ASN][1000 genomes]
rs10874752	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11164827	0.81[CEU][hapmap]
rs11164838	0.81[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs11164848	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164849	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164850	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11164851	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11164854	0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs12049007	0.93[ASN][1000 genomes]
rs12092304	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12120036	0.93[ASN][1000 genomes]
rs12130044	0.93[ASN][1000 genomes]
rs12144226	0.84[ASN][1000 genomes]
rs12747275	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1678784	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2086314	0.93[ASN][1000 genomes]
rs2127398	0.93[ASN][1000 genomes]
rs2127400	0.93[ASN][1000 genomes]
rs28561471	0.82[ASN][1000 genomes]
rs3943283	0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs4515797	0.84[ASN][1000 genomes]
rs4847226	0.92[ASN][1000 genomes]
rs4847386	0.88[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4847389	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs514235	1.00[CEU][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs521428	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534409	0.84[ASN][1000 genomes]
rs567613	0.87[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579800	0.82[EUR][1000 genomes]
rs594527	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606344	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641462	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs655026	0.81[EUR][1000 genomes]
rs660870	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663112	0.91[ASN][1000 genomes]
rs6671078	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6671268	1.00[CEU][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6681240	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6681345	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7517539	0.84[ASN][1000 genomes]
rs7524934	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs753391	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs770883	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs770884	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs945630	0.82[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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs619784	CDC73	trans	cerebellum	SCAN
rs619784	BARHL2	cis	parietal	SCAN
rs619784	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93448000-93454800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:93448000-93454800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:93448800-93454600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:93449000-93454400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:93451800-93466000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:93452400-93458600	Weak transcription	HSMMtube	muscle
7	chr1:93452600-93456000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:93453800-93456200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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