Variant report

Variant	rs2173117
Chromosome Location	chr8:11605130-11605131
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10435714	0.83[EUR][1000 genomes]
rs2029969	0.80[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2645400	0.89[CHD][hapmap]
rs3729848	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs3735816	1.00[JPT][hapmap]
rs3735818	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3779664	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4841587	0.82[ASN][1000 genomes]
rs4841588	0.89[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs804282	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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 target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv890359	chr8:11599570-11617240	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2173117	AMAC1L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11602000-11606600	Enhancers	Ovary	ovary
2	chr8:11602400-11606000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:11602400-11606200	Weak transcription	Right Ventricle	heart
4	chr8:11604400-11605800	Enhancers	Pancreas	Pancrea
5	chr8:11604400-11609000	Strong transcription	Fetal Intestine Small	intestine
6	chr8:11604400-11614400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:11604600-11605200	Enhancers	Stomach Mucosa	stomach
8	chr8:11604600-11606200	Weak transcription	HepG2	liver
9	chr8:11604600-11606400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr8:11604600-11609600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr8:11604800-11605800	Weak transcription	Liver	Liver
12	chr8:11604800-11607200	Enhancers	Fetal Heart	heart
13	chr8:11604800-11616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr8:11605000-11605600	Weak transcription	Gastric	stomach
15	chr8:11605000-11606400	Weak transcription	Left Ventricle	heart
16	chr8:11605000-11612400	Weak transcription	Fetal Intestine Large	intestine

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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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