Variant report

Variant	rs2906859
Chromosome Location	chr12:68396135-68396136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:68396000-68396150	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RPL39P28	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1019076	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878723	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11177002	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11177008	0.91[EUR][1000 genomes]
rs12228471	0.88[EUR][1000 genomes]
rs12582272	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1468487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17104682	0.95[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2051993	0.92[EUR][1000 genomes]
rs2860609	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2870960	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2906853	0.81[AFR][1000 genomes]
rs2906854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2906856	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2906862	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015002	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56393928	0.88[EUR][1000 genomes]
rs61923060	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7306466	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7952790	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7962511	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[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	esv3411149	chr12:68066948-68435533	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1039638	chr12:68293351-68399871	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv975509	chr12:68382193-68405026	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2906859	FRS2	cis	parietal	SCAN
rs2906859	IFNG-AS1	cis	Whole Blood	GTEx
rs2906859	IFNG-AS1	cis	Muscle Skeletal	GTEx
rs2906859	CPM	cis	parietal	SCAN
rs2906859	IFNG-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68386400-68404200	Weak transcription	Primary B cells from cord blood	blood
2	chr12:68386800-68404600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:68391400-68405400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:68392400-68404600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:68392400-68404800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:68392600-68413800	Weak transcription	Primary T cells from cord blood	blood
7	chr12:68392800-68405200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:68393000-68405000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:68395800-68398200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:68395800-68404400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:68396000-68396200	Enhancers	Liver	Liver

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