Variant report

Variant	rs4683505
Chromosome Location	chr3:140247177-140247178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12054019	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12488519	0.84[EUR][1000 genomes]
rs12494276	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs168387	0.88[CHD][hapmap]
rs16850356	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap]
rs16850427	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs180971	0.89[CHD][hapmap]
rs349503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs349508	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs349543	0.84[EUR][1000 genomes]
rs349547	1.00[CEU][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[ASN][1000 genomes]
rs349565	0.86[CHD][hapmap]
rs349566	0.89[CHD][hapmap]
rs349567	0.89[CHD][hapmap]
rs349568	0.81[CHD][hapmap]
rs4683500	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4683506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs495109	1.00[CEU][hapmap]
rs536892	1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs544827	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58159053	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72632312	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72632313	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72632314	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7433000	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9857310	1.00[CEU][hapmap]

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	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv591863	chr3:140126067-140274442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2753648	chr3:140247073-140250708	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Myopia (pathological)	23049088	GWAS catalog

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140224400-140247200	Weak transcription	Ovary	ovary
2	chr3:140237400-140249400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:140242200-140249400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:140243400-140247600	Weak transcription	HSMMtube	muscle
5	chr3:140245400-140250000	Enhancers	HSMM	muscle
6	chr3:140245600-140251200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:140245800-140251000	Enhancers	HMEC	breast
8	chr3:140246600-140247600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:140247000-140250000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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