Variant report

Variant	rs592056
Chromosome Location	chr6:140256857-140256858
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	chr6:139694684..139697873-chr6:140255144..140258596,3	K562	blood:
2	chr6:140256563..140258976-chr6:140261576..140263079,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1028469	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525047	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12526885	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12663217	0.95[ASN][1000 genomes]
rs12663483	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12665399	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13194827	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13204837	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1416289	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1933742	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1953788	1.00[ASN][1000 genomes]
rs1953789	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs586246	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587235	0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592440	0.81[EUR][1000 genomes]
rs598498	0.85[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs599378	0.82[AMR][1000 genomes]
rs603310	0.81[EUR][1000 genomes]
rs607284	0.81[EUR][1000 genomes]
rs609488	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs616279	0.89[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622216	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62429515	0.98[ASN][1000 genomes]
rs62429516	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62429517	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs647968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648510	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs650774	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs67013338	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs679849	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680290	0.85[CHB][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681235	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926807	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6928433	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs724061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7743656	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs856646	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373255	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9376482	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9385888	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9389733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9399298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9399299	0.99[ASN][1000 genomes]
rs9403134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9495636	0.88[YRI][hapmap]
rs9495641	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs592056	CITED2	cis	parietal	SCAN
rs592056	HIVEP2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140242400-140260200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:140254800-140259200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:140255000-140258400	Weak transcription	K562	blood
4	chr6:140255000-140262200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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