Variant report

Variant	rs12079988
Chromosome Location	chr1:86763077-86763078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11161796	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11161797	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11799749	1.00[MKK][hapmap]
rs11801454	1.00[AMR][1000 genomes]
rs11803763	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804733	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11810074	1.00[AMR][1000 genomes]
rs12096446	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34372019	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56841249	1.00[AMR][1000 genomes]
rs59696140	0.82[AFR][1000 genomes]
rs72949810	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949857	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949858	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949874	1.00[AMR][1000 genomes]
rs72949879	1.00[AMR][1000 genomes]
rs72949884	1.00[AMR][1000 genomes]
rs72949902	1.00[AMR][1000 genomes]
rs72951825	1.00[AMR][1000 genomes]
rs72951830	1.00[AMR][1000 genomes]
rs72951832	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871223	chr1:86724523-86784804	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12079988	CD3D	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86761600-86763200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:86761800-86763200	Enhancers	HSMMtube	muscle
3	chr1:86762000-86763200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:86762800-86771400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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