Variant report

Variant	rs12799376
Chromosome Location	chr11:71880658-71880659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10898824	0.81[ASN][1000 genomes]
rs11235461	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11235463	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11235465	0.82[AMR][1000 genomes]
rs11235466	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12799010	0.83[EUR][1000 genomes]
rs2071010	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34030891	0.94[AMR][1000 genomes]
rs34180002	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34465999	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34607504	0.81[EUR][1000 genomes]
rs35954619	0.83[EUR][1000 genomes]
rs36083292	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36147472	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67805606	0.83[EUR][1000 genomes]
rs7934420	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	esv3493111	chr11:71850822-71893073	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3493112	chr11:71850822-71893073	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv435918	chr11:71851427-71890983	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv5948	chr11:71851479-71890582	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3359634	chr11:71851533-71892403	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2513904	chr11:71852934-71892793	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12799376	ARAP1-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71875200-71884200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:71879800-71881800	Enhancers	Fetal Intestine Large	intestine
3	chr11:71879800-71882200	Enhancers	Fetal Intestine Small	intestine
4	chr11:71880000-71880800	Enhancers	Placenta	Placenta
5	chr11:71880000-71881000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:71880000-71881000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:71880000-71881000	Enhancers	Colonic Mucosa	Colon
8	chr11:71880000-71882000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr11:71880400-71881200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr11:71880400-71881200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr11:71880400-71881400	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:71880400-71881600	Enhancers	Brain Hippocampus Middle	brain
13	chr11:71880400-71883400	Weak transcription	HMEC	breast
14	chr11:71880600-71880800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:71880600-71881200	Enhancers	Brain Substantia Nigra	brain
16	chr11:71880600-71883000	Weak transcription	NHEK	skin

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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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