Variant report

Variant	rs11516173
Chromosome Location	chr12:123927262-123927263
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs28434767	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28613184	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35416759	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11516173	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs11516173	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs11516173	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs11516173	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123921800-123928600	Weak transcription	HepG2	liver
2	chr12:123921800-123928800	Weak transcription	Right Atrium	heart
3	chr12:123921800-123929600	Weak transcription	Spleen	Spleen
4	chr12:123921800-123930200	Weak transcription	Pancreas	Pancrea
5	chr12:123921800-123930400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:123922400-123927400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:123922400-123928800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:123922600-123928400	Weak transcription	Lung	lung
9	chr12:123922600-123929000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:123926200-123929400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:123926200-123932800	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:123926200-123933000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:123926400-123928200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:123926600-123930200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr12:123926800-123928400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:123927200-123927600	Flanking Active TSS	GM12878-XiMat	blood
17	chr12:123927200-123927800	Enhancers	Primary B cells from cord blood	blood
18	chr12:123927200-123927800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr12:123927200-123929400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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