Variant report

Variant	rs2906856
Chromosome Location	chr12:68390201-68390202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1019076	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878723	0.83[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11177002	0.83[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12582272	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1468487	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2159064	0.89[EUR][1000 genomes]
rs2860609	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2906854	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2906859	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2906862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3015001	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3015002	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923060	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7306466	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7952790	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7962511	0.83[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.85[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
rs2906856	IFNG-AS1	cis	Muscle Skeletal	GTEx
rs2906856	IFNG-AS1	cis	Whole Blood	GTEx
rs2906856	IFNG-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:12 , 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	chr12:68386200-68391800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:68386400-68404200	Weak transcription	Primary B cells from cord blood	blood
5	chr12:68386600-68391800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:68386800-68404600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:68387000-68392200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:68387000-68395000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:68388600-68392000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:68389600-68390400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:68390000-68390600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:68390200-68390400	Enhancers	Osteobl	bone

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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