Variant report

Variant	rs2170404
Chromosome Location	chr3:98722587-98722588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1082403	0.81[ASN][1000 genomes]
rs1082405	0.81[ASN][1000 genomes]
rs10935514	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs10935587	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12632798	0.87[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs13316760	0.96[CEU][hapmap];0.84[JPT][hapmap]
rs1371687	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1383906	0.82[ASN][1000 genomes]
rs1383907	0.82[ASN][1000 genomes]
rs1481631	0.81[ASN][1000 genomes]
rs2062058	0.82[YRI][hapmap]
rs2128052	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439237	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs2449046	0.81[ASN][1000 genomes]
rs2449063	0.80[CHB][hapmap]
rs2462234	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs2462239	0.80[CHB][hapmap]
rs2470759	0.80[CHB][hapmap]
rs2470761	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs2470770	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2470814	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470873	0.82[ASN][1000 genomes]
rs2470877	0.82[ASN][1000 genomes]
rs2470880	0.82[ASN][1000 genomes]
rs278379	0.92[CEU][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs278380	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs278381	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs278382	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs278387	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs278388	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs35936923	0.88[ASN][1000 genomes]
rs4857416	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6774875	0.84[JPT][hapmap]
rs7615628	0.89[JPT][hapmap];0.81[YRI][hapmap]
rs7615856	0.92[CEU][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs774544	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs774547	0.81[ASN][1000 genomes]
rs828614	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs828616	0.84[JPT][hapmap]
rs828617	0.92[CEU][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap]
rs828621	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs852701	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs955351	0.96[CEU][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs964163	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv980100	chr3:98714787-98766962	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2170404	ZBTB11	cis	cerebellum	SCAN
rs2170404	DCBLD2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98712800-98723000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:98717200-98730600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:98717600-98729200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:98721600-98724200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:98721800-98726200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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