Variant report

Variant	rs6475265
Chromosome Location	chr9:18869492-18869493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10124966	0.81[AMR][1000 genomes]
rs10756996	0.84[CEU][hapmap]
rs1359843	0.85[CEU][hapmap]
rs1368772	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1433826	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1433829	0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1433831	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2104596	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3780222	0.85[CEU][hapmap]
rs3866508	0.83[AMR][1000 genomes]
rs4977454	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4977460	0.80[EUR][1000 genomes]
rs7026374	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7031202	0.87[AMR][1000 genomes]
rs731370	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7873965	0.81[EUR][1000 genomes]
rs7874517	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs934482	0.96[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.83[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	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
5	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892698	chr9:18830444-18905289	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6475265	IFNB1	cis	cerebellum	SCAN
rs6475265	TGM6	trans	parietal	SCAN
rs6475265	RRAGA	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18858800-18876600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:18862800-18870000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:18863000-18871200	Strong transcription	HSMM	muscle
4	chr9:18863800-18881800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:18864400-18883000	Weak transcription	NH-A	brain
6	chr9:18867000-18872800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:18868000-18872200	Strong transcription	Osteobl	bone
8	chr9:18868200-18869600	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr9:18868800-18869800	ZNF genes & repeats	NHDF-Ad	bronchial
10	chr9:18869000-18869600	ZNF genes & repeats	Fetal Stomach	stomach
11	chr9:18869000-18870600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:18869200-18869600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:18869400-18887800	Weak transcription	Aorta	Aorta

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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