Variant report

Variant	rs1016245
Chromosome Location	chr6:142167858-142167859
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1015163	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192435	0.91[EUR][1000 genomes]
rs12202995	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12209597	0.81[AMR][1000 genomes]
rs2064481	0.92[EUR][1000 genomes]
rs2207235	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223924	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35461728	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67686972	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6916753	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6917355	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6927997	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6936548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6940233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7450452	0.86[EUR][1000 genomes]
rs7750605	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755310	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7762021	0.86[EUR][1000 genomes]
rs9285495	0.90[EUR][1000 genomes]
rs9321840	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9321841	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484552	0.87[EUR][1000 genomes]
rs9484553	0.87[EUR][1000 genomes]
rs9484557	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9484558	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9484559	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9484564	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9484565	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496143	0.87[EUR][1000 genomes]
rs9496146	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9496163	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9496164	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9496166	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496167	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496168	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015835	chr6:141713451-142233317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv538455	chr6:141713451-142233317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032184	chr6:141909953-142234993	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1032444	chr6:142066183-142199093	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv830823	chr6:142111420-142305417	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv464066	chr6:142130009-142236578	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv604790	chr6:142130009-142236578	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv886728	chr6:142130009-142245981	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1029504	chr6:142131846-142333198	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv538458	chr6:142131846-142333198	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1017195	chr6:142142454-142336722	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1016245	CITED2	cis	parietal	SCAN
rs1016245	HEBP2	cis	cerebellum	SCAN
rs1016245	AIG1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142167000-142170400	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr6:142167000-142170600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:142167200-142170600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:142167200-142170800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr6:142167400-142170600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr6:142167400-142170800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:142167400-142170800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr6:142167400-142170800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr6:142167400-142171600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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