Variant report

Variant	rs10840160
Chromosome Location	chr11:9053536-9053537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10769979	0.83[CHD][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs11042125	0.81[MEX][hapmap]
rs11042151	0.86[MEX][hapmap];0.89[TSI][hapmap]
rs11042154	0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap]
rs1560569	0.81[TSI][hapmap]
rs1984791	0.83[CHB][hapmap];0.80[CHD][hapmap];0.82[ASN][1000 genomes]
rs2016942	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2653570	0.83[CHD][hapmap];0.81[TSI][hapmap]
rs2653605	0.83[CHD][hapmap]
rs4910442	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486060	0.86[TSI][hapmap]
rs7479407	0.86[MEX][hapmap];0.92[TSI][hapmap]
rs7925728	0.83[CHD][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]

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	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10840160	RRP8	cis	parietal	SCAN
rs10840160	NRIP3	cis	parietal	SCAN
rs10840160	AKIP1	cis	Thyroid	GTEx
rs10840160	ST5	cis	parietal	SCAN
rs10840160	RPL27A	cis	parietal	SCAN
rs10840160	TMEM9B-AS1	cis	lung	GTEx
rs10840160	WEE1	cis	parietal	SCAN
rs10840160	OR52A1	cis	parietal	SCAN
rs10840160	SNORA3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9038200-9064000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr11:9039000-9058800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:9039600-9057800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:9043400-9059200	Weak transcription	Right Atrium	heart
5	chr11:9047200-9068600	Weak transcription	Fetal Intestine Large	intestine
6	chr11:9047800-9058400	Weak transcription	HSMMtube	muscle
7	chr11:9049000-9056600	Weak transcription	Fetal Lung	lung
8	chr11:9051200-9054000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:9051400-9059000	Weak transcription	Placenta	Placenta
10	chr11:9052400-9067800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:9052600-9055000	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:9052800-9054200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:9052800-9054800	Weak transcription	Adipose Nuclei	Adipose
14	chr11:9052800-9055000	Weak transcription	Pancreas	Pancrea
15	chr11:9052800-9058000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:9052800-9060400	Weak transcription	Lung	lung
17	chr11:9052800-9060600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:9052800-9069800	Weak transcription	Gastric	stomach
19	chr11:9053000-9060600	Weak transcription	Fetal Stomach	stomach

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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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