Variant report

Variant	rs28398784
Chromosome Location	chr3:119854624-119854625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119813993..119815567-chr3:119852618..119855030,3	MCF-7	breast:
2	chr3:119813608..119816143-chr3:119854380..119857222,6	MCF-7	breast:
3	chr3:119847191..119849772-chr3:119853713..119855581,2	K562	blood:
4	chr3:119854307..119856524-chr3:119867161..119869039,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10049256	0.86[EUR][1000 genomes]
rs10934512	0.86[EUR][1000 genomes]
rs10934514	0.81[EUR][1000 genomes]
rs10934515	0.86[EUR][1000 genomes]
rs10934516	0.86[EUR][1000 genomes]
rs10934517	0.86[EUR][1000 genomes]
rs11707711	0.86[EUR][1000 genomes]
rs12152218	0.84[EUR][1000 genomes]
rs1352458	0.86[EUR][1000 genomes]
rs1488761	0.86[EUR][1000 genomes]
rs1488762	0.86[EUR][1000 genomes]
rs1488764	0.86[EUR][1000 genomes]
rs1907681	0.86[EUR][1000 genomes]
rs2035671	0.86[EUR][1000 genomes]
rs2035672	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2035673	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2035674	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2130000	0.86[EUR][1000 genomes]
rs2130001	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2171598	0.86[EUR][1000 genomes]
rs2171599	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2319541	0.86[EUR][1000 genomes]
rs2319542	0.86[EUR][1000 genomes]
rs2319543	0.86[EUR][1000 genomes]
rs2874022	0.86[EUR][1000 genomes]
rs2874023	0.86[EUR][1000 genomes]
rs3112282	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3112283	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs334539	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs334540	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs334545	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs334549	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4488869	0.91[EUR][1000 genomes]
rs4676804	0.86[EUR][1000 genomes]
rs4676809	0.86[EUR][1000 genomes]
rs4676822	0.86[EUR][1000 genomes]
rs4676832	0.82[EUR][1000 genomes]
rs6438558	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438559	0.91[EUR][1000 genomes]
rs6438561	0.80[EUR][1000 genomes]
rs6438562	0.84[EUR][1000 genomes]
rs6438564	0.86[EUR][1000 genomes]
rs6438566	0.86[EUR][1000 genomes]
rs6438567	0.86[EUR][1000 genomes]
rs6764549	0.86[EUR][1000 genomes]
rs6769988	0.89[EUR][1000 genomes]
rs6776122	0.86[EUR][1000 genomes]
rs6777971	0.82[EUR][1000 genomes]
rs6781470	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782570	0.91[EUR][1000 genomes]
rs6794478	0.91[EUR][1000 genomes]
rs6805050	0.86[EUR][1000 genomes]
rs7637828	0.86[EUR][1000 genomes]
rs7641838	0.86[EUR][1000 genomes]
rs7642171	0.84[EUR][1000 genomes]
rs7644268	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653263	0.86[EUR][1000 genomes]
rs7653396	0.86[EUR][1000 genomes]
rs901920	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902790	0.86[EUR][1000 genomes]
rs902791	0.86[EUR][1000 genomes]
rs902792	0.86[EUR][1000 genomes]
rs902794	0.86[EUR][1000 genomes]
rs902795	0.93[EUR][1000 genomes]
rs923380	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923726	0.86[EUR][1000 genomes]
rs923727	0.86[EUR][1000 genomes]
rs923728	0.86[EUR][1000 genomes]
rs9289142	0.86[EUR][1000 genomes]
rs9289143	0.86[EUR][1000 genomes]
rs979682	0.86[EUR][1000 genomes]
rs9813834	0.86[EUR][1000 genomes]
rs9841122	0.86[EUR][1000 genomes]
rs9842302	0.86[EUR][1000 genomes]
rs9849023	0.81[EUR][1000 genomes]
rs9853082	0.86[EUR][1000 genomes]
rs9857123	0.86[EUR][1000 genomes]
rs9858566	0.86[EUR][1000 genomes]
rs9868058	0.83[EUR][1000 genomes]
rs9868312	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119836800-119860800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:119844200-119863400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:119851400-119856400	Weak transcription	Pancreas	Pancrea
4	chr3:119853800-119855200	Enhancers	Placenta	Placenta
5	chr3:119854000-119855000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:119854200-119854800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:119854200-119854800	Enhancers	Hela-S3	cervix
8	chr3:119854200-119854800	Enhancers	HMEC	breast
9	chr3:119854200-119854800	Enhancers	HUVEC	blood vessel
10	chr3:119854200-119855000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:119854200-119855000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:119854200-119855200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:119854200-119855200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:119854200-119855200	Enhancers	NHEK	skin
15	chr3:119854200-119855400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:119854200-119856000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:119854400-119855000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr3:119854400-119855800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:119854400-119863200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:119854600-119863000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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