Variant report

Variant	rs7116227
Chromosome Location	chr11:86010856-86010857
allele	A/G
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]
rs11234604	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11820048	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11820262	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11820306	1.00[ASN][1000 genomes]
rs11822824	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11823516	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11823646	0.81[AFR][1000 genomes]
rs11825208	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2167611	0.97[ASN][1000 genomes]
rs3758879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57089989	0.91[AFR][1000 genomes]
rs57381996	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7115858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118858	0.86[ASN][1000 genomes]
rs7129295	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931249	1.00[ASN][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	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv508643	chr11:85988577-86047719	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv519914	chr11:86010789-86013361	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7116227	HIRA	trans	lymphoblastoid	RTeQTL
rs7116227	MRPL40	trans	lymphoblastoid	RTeQTL
rs7116227	SNAP29	trans	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85995600-86012600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:85995600-86012800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr11:85995800-86012600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:85995800-86013200	Weak transcription	Esophagus	oesophagus
5	chr11:85995800-86013200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:85996000-86012800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:85996000-86013000	Weak transcription	Fetal Intestine Large	intestine
8	chr11:86003000-86012600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:86003200-86013000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:86005400-86012600	Weak transcription	GM12878-XiMat	blood
11	chr11:86010400-86011200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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