Variant report

Variant	rs1832747
Chromosome Location	chr9:18487744-18487745
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10217409	0.87[EUR][1000 genomes]
rs10217753	0.84[ASW][hapmap];0.88[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10756964	0.82[EUR][1000 genomes]
rs10810969	0.80[EUR][1000 genomes]
rs10810971	0.81[EUR][1000 genomes]
rs10810973	0.92[ASN][1000 genomes]
rs10963613	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs11793923	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1281350	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1281352	0.92[ASN][1000 genomes]
rs1329720	0.80[CHD][hapmap]
rs1329721	0.80[EUR][1000 genomes]
rs1340040	0.81[EUR][1000 genomes]
rs1888067	0.87[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2153415	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2153416	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4961650	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4961651	0.92[ASN][1000 genomes]
rs4961652	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4961653	0.88[CEU][hapmap];0.81[LWK][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4961654	0.80[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6475216	0.81[EUR][1000 genomes]
rs6475221	0.92[ASN][1000 genomes]
rs7019399	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7856703	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7864856	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv892689	chr9:18485434-18537444	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv892690	chr9:18485434-18592374	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1832747	CNTLN	cis	cerebellum	SCAN
rs1832747	KIAA1797	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18477400-18489200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:18479200-18490000	Weak transcription	Aorta	Aorta
3	chr9:18482600-18492200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:18485400-18488600	Weak transcription	HUVEC	blood vessel
5	chr9:18485800-18490800	Weak transcription	Fetal Brain Female	brain
6	chr9:18486000-18488400	Weak transcription	NH-A	brain
7	chr9:18486000-18488800	Weak transcription	NHLF	lung
8	chr9:18486000-18490000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:18486000-18490000	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:18486000-18490200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:18486000-18490400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:18486200-18488600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:18486200-18490000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:18486200-18490000	Weak transcription	Fetal Stomach	stomach
15	chr9:18486200-18490800	Weak transcription	Fetal Lung	lung
16	chr9:18486400-18488800	Weak transcription	HSMMtube	muscle
17	chr9:18486600-18488000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:18486600-18489200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:18486800-18488000	Strong transcription	HSMM	muscle
20	chr9:18487200-18487800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:18487200-18488400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:18487200-18490200	Enhancers	Osteobl	bone
23	chr9:18487400-18488000	Enhancers	Adipose Nuclei	Adipose
24	chr9:18487400-18488000	Genic enhancers	NHDF-Ad	bronchial
25	chr9:18487400-18495600	Enhancers	Fetal Heart	heart
26	chr9:18487600-18487800	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr9:18487600-18487800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:18487600-18487800	Enhancers	Ovary	ovary
29	chr9:18487600-18488200	Enhancers	Colon Smooth Muscle	Colon

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