Variant report

Variant	rs3898100
Chromosome Location	chr9:18468875-18468876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1006022	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10453192	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10733354	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10738511	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756965	0.92[ASN][1000 genomes]
rs10756966	0.92[ASN][1000 genomes]
rs10756967	0.92[ASN][1000 genomes]
rs10810972	0.92[AFR][1000 genomes]
rs10810973	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10963613	0.85[CEU][hapmap]
rs11793923	0.96[CEU][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1281352	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1329720	0.82[CHB][hapmap]
rs1340039	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1341063	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1417035	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1417037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1538999	0.89[CEU][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs16936745	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16936779	0.82[CHB][hapmap]
rs1888067	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1888068	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1888069	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1999174	0.93[ASN][1000 genomes]
rs2000047	0.93[ASN][1000 genomes]
rs2149875	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2153415	0.96[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2153416	0.96[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2277160	0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4246142	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4246143	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4590536	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4961649	0.93[ASN][1000 genomes]
rs4961651	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4961652	0.96[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4961653	0.86[CHB][hapmap]
rs4961654	0.81[CHB][hapmap]
rs6475219	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6475220	0.94[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6475221	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7019399	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7032393	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7036515	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7046502	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7856703	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7864727	0.82[JPT][hapmap]
rs7867766	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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
rs3898100	FREM1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18464200-18469400	Weak transcription	NHDF-Ad	bronchial
2	chr9:18464200-18471600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:18464200-18474400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:18464400-18469000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:18464400-18473000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:18466400-18471800	Weak transcription	Hela-S3	cervix
7	chr9:18468800-18470200	Weak transcription	Fetal Heart	heart

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