Variant report

Variant	rs2906854
Chromosome Location	chr12:68387346-68387347
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	chr12:68379962..68383054-chr12:68386184..68387987,3	MCF-7	breast:
2	chr12:68386083..68387816-chr12:68389627..68392422,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1019076	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878723	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11177002	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11177008	0.90[EUR][1000 genomes]
rs12228471	0.87[EUR][1000 genomes]
rs12582272	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1468487	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17104682	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2051993	0.92[EUR][1000 genomes]
rs2860609	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2870960	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2906853	0.82[AFR][1000 genomes]
rs2906856	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2906859	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2906862	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3015001	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3015002	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56393928	0.87[EUR][1000 genomes]
rs61923060	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7306466	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7952790	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7962511	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2906854	IFNG-AS1	cis	Muscle Skeletal	GTEx
rs2906854	IFNG-AS1	cis	Whole Blood	GTEx
rs2906854	IFNG-AS1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68385600-68391000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:68385600-68392000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:68386200-68387600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:68386200-68391800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:68386400-68404200	Weak transcription	Primary B cells from cord blood	blood
6	chr12:68386600-68391800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:68386800-68404600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:68387000-68392200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:68387000-68395000	Weak transcription	Primary B cells from peripheral blood	blood

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