Variant report

Variant	rs12797787
Chromosome Location	chr11:86555189-86555190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12785531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12792551	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12795324	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12797823	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12799759	0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs12800507	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12801911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12802654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12804499	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12807497	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12808837	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34164281	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34168253	1.00[AMR][1000 genomes]
rs34926341	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35029679	0.81[EUR][1000 genomes]
rs35322327	0.81[EUR][1000 genomes]
rs56241897	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2756074	chr11:86456552-86729552	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv975959	chr11:86534725-86568919	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1836220	chr11:86542005-86573310	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12797787	ABCB9	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86537200-86580600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:86542800-86555400	Weak transcription	Fetal Lung	lung
3	chr11:86543200-86582600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:86547800-86562400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:86549600-86581400	Weak transcription	Ovary	ovary
6	chr11:86549800-86557200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:86549800-86562400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:86549800-86576400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:86550000-86557400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:86550000-86575200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:86550600-86559000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:86551200-86557200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:86554200-86557200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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Input of quick search could be:

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

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