Variant report

Variant	rs9838800
Chromosome Location	chr3:191128546-191128547
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10513865	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1369278	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs1369279	0.84[CHB][hapmap]
rs1474188	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16822368	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16822380	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16822451	1.00[ASN][1000 genomes]
rs16848976	0.95[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs16866501	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs16866503	0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs16866506	0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs17811727	0.86[TSI][hapmap]
rs2117548	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2293379	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs293810	0.83[CHD][hapmap]
rs293840	0.84[CHD][hapmap]
rs420266	0.84[CHD][hapmap]
rs4247190	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs436393	0.84[CHD][hapmap]
rs438589	0.84[CHD][hapmap]
rs4677633	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4677731	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4687210	0.81[TSI][hapmap]
rs58077600	0.84[ASN][1000 genomes]
rs58631024	0.95[ASN][1000 genomes]
rs58648691	0.95[ASN][1000 genomes]
rs59491001	0.98[ASN][1000 genomes]
rs60089463	0.95[ASN][1000 genomes]
rs60176909	0.96[ASN][1000 genomes]
rs60204557	0.84[ASN][1000 genomes]
rs9812544	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9832656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844500	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854318	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868286	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9838800	GP5	cis	parietal	SCAN
rs9838800	CCDC50	cis	Esophagus Muscularis	GTEx
rs9838800	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:191118400-191130000	Weak transcription	NH-A	brain
4	chr3:191127200-191129400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
5	chr3:191127400-191130800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:191128400-191129000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:191128400-191129000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:191128400-191129400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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