Variant report

Variant	rs2153416
Chromosome Location	chr9:18485191-18485192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1006022	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10217753	0.80[CHD][hapmap]
rs10453192	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10733354	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10738511	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10810972	0.85[AFR][1000 genomes]
rs10810973	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963613	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs1147795	0.88[YRI][hapmap]
rs11793923	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281350	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs1281352	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1340039	0.84[EUR][1000 genomes]
rs1417035	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1417037	0.96[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1538999	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16936745	0.85[CEU][hapmap]
rs1832747	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1888068	0.96[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1888069	0.96[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2149875	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2153415	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277160	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3898100	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4246142	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4246143	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4590536	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4961650	0.89[ASN][1000 genomes]
rs4961651	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4961652	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4961654	0.81[CHD][hapmap]
rs6475219	0.88[EUR][1000 genomes]
rs6475220	0.92[CEU][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6475221	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7019399	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7032393	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7036515	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7046502	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7856703	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7864856	0.92[ASN][1000 genomes]
rs7867766	0.92[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2153416	FREM1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18476000-18485600	Weak transcription	Fetal Stomach	stomach
2	chr9:18477400-18489200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:18479000-18485200	Weak transcription	Fetal Heart	heart
4	chr9:18479200-18490000	Weak transcription	Aorta	Aorta
5	chr9:18480600-18485600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:18480800-18485600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:18481400-18485200	Weak transcription	NH-A	brain
8	chr9:18482600-18492200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:18482800-18485600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:18483400-18485200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:18484000-18486000	Genic enhancers	NHDF-Ad	bronchial
12	chr9:18484000-18486800	Genic enhancers	HSMM	muscle
13	chr9:18484400-18486200	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr9:18484400-18486200	Enhancers	Colon Smooth Muscle	Colon
15	chr9:18484600-18485400	Enhancers	HUVEC	blood vessel
16	chr9:18484600-18485600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:18484600-18486000	Enhancers	Fetal Muscle Leg	muscle
18	chr9:18484600-18486000	Enhancers	Stomach Smooth Muscle	stomach
19	chr9:18484800-18485200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:18484800-18485600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:18485000-18485400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:18485000-18485400	Weak transcription	HSMMtube	muscle
23	chr9:18485000-18485400	Strong transcription	Osteobl	bone

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