Variant report

Variant	rs2515066
Chromosome Location	chr8:119431673-119431674
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10505334	1.00[GIH][hapmap]
rs17829264	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2514984	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2514987	0.95[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2514988	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2514989	0.95[CEU][hapmap];0.85[CHB][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2514992	0.90[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2514994	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57762320	0.86[AMR][1000 genomes]
rs7002648	0.96[GIH][hapmap]

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	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1032681	chr8:119153316-119609948	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv539737	chr8:119153316-119609948	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1016379	chr8:119164234-119448910	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv831443	chr8:119390590-119590662	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2515066	KHDC1	cis	Liver	GTEx
rs2515066	SAMD12	cis	multi-tissue	Pritchard
rs2515066	C6orf148	trans	multi-tissue	Pritchard
rs2515066	PMS2L1	trans	multi-tissue	Pritchard
rs2515066	PMS2L1	cis	Liver	GTEx
rs2515066	SAMD12	cis	Liver	GTEx
rs2515066	TXK	cis	Liver	GTEx
rs2515066	TXK	trans	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119428400-119431800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:119428400-119433600	Weak transcription	Fetal Heart	heart
3	chr8:119429200-119432000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:119429600-119432400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:119431000-119431800	Enhancers	A549	lung
6	chr8:119431200-119431800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr8:119431200-119431800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr8:119431200-119431800	Enhancers	HUVEC	blood vessel
9	chr8:119431200-119432000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr8:119431200-119432000	Enhancers	NHDF-Ad	bronchial
11	chr8:119431400-119432400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:119431600-119432000	Enhancers	Hela-S3	cervix

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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