Variant report

Variant	rs2929491
Chromosome Location	chr3:98716519-98716520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98536130..98536715-chr3:98716022..98716899,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1082398	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082399	1.00[EUR][1000 genomes]
rs1082400	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082402	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082404	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082406	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1351496	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1383908	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1440157	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs1481633	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1600788	0.82[AFR][1000 genomes]
rs1818053	0.86[YRI][hapmap]
rs1972432	0.84[AFR][1000 genomes]
rs2128053	0.84[AFR][1000 genomes]
rs2133575	0.82[AFR][1000 genomes]
rs2173598	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2439234	0.86[YRI][hapmap]
rs2439235	0.86[YRI][hapmap]
rs2448985	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2454681	0.84[AFR][1000 genomes]
rs2454683	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2470820	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2470828	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2470856	0.84[AFR][1000 genomes]
rs2470858	0.82[AFR][1000 genomes]
rs2470868	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2470883	0.84[AFR][1000 genomes]
rs2470884	0.82[AFR][1000 genomes]
rs4273318	0.84[AFR][1000 genomes]
rs4857107	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs5013928	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs6795351	0.85[AFR][1000 genomes]
rs73858658	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7630797	0.81[AFR][1000 genomes]
rs774536	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774543	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774546	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774548	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	0.85[YRI][hapmap]
rs828607	0.86[YRI][hapmap]
rs974982	0.97[AFR][1000 genomes]
rs9883226	0.86[YRI][hapmap]
rs996199	0.86[YRI][hapmap];0.82[AFR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98711000-98721200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:98712800-98723000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:98713200-98721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:98716400-98717200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:98716400-98717600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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