Variant report

Variant	rs9819865
Chromosome Location	chr3:24636524-24636525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24534908..24536428-chr3:24635223..24637063,2	MCF-7	breast:
2	chr3:24631935..24633898-chr3:24636048..24638829,2	MCF-7	breast:
3	chr3:24562239..24564510-chr3:24636184..24637774,2	MCF-7	breast:
4	chr3:24535097..24538455-chr3:24631744..24636761,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction
ENSG00000265028	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10212332	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10490837	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs11712286	0.88[CEU][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13318800	0.85[ASN][1000 genomes]
rs1561079	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17014900	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs17014902	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs1992040	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1992041	0.85[ASN][1000 genomes]
rs2043578	0.88[CEU][hapmap]
rs2117873	0.86[ASN][1000 genomes]
rs2196434	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2196438	0.91[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs28562279	0.93[ASN][1000 genomes]
rs3919672	0.86[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap]
rs56268655	0.85[ASN][1000 genomes]
rs58152527	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61701305	0.99[ASN][1000 genomes]
rs6550878	0.96[ASN][1000 genomes]
rs6550879	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6767534	0.88[ASN][1000 genomes]
rs6767717	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769209	0.95[ASN][1000 genomes]
rs6770518	0.94[ASN][1000 genomes]
rs6771818	0.95[ASN][1000 genomes]
rs6781066	0.96[ASN][1000 genomes]
rs6795607	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6801494	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040438	0.86[ASN][1000 genomes]
rs7618528	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7647700	0.85[ASN][1000 genomes]
rs930317	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9310745	0.86[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9823545	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9830859	0.91[CHB][hapmap];0.95[ASN][1000 genomes]
rs9835497	0.86[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9838616	0.96[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9838720	0.96[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9843609	0.83[ASN][1000 genomes]
rs9844544	0.84[ASN][1000 genomes]
rs9850781	0.85[ASN][1000 genomes]
rs9853927	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs9859978	0.93[ASN][1000 genomes]
rs9861129	0.84[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs9868375	0.92[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs9873830	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs9878606	0.85[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9819865	RPL15	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24630800-24640800	Weak transcription	Small Intestine	intestine
2	chr3:24632000-24637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:24632000-24640000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:24632200-24637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:24633200-24640000	Weak transcription	Fetal Lung	lung
6	chr3:24633600-24637000	Weak transcription	Stomach Mucosa	stomach
7	chr3:24633600-24640000	Weak transcription	NHDF-Ad	bronchial
8	chr3:24633800-24637200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:24633800-24639600	Weak transcription	HUVEC	blood vessel
10	chr3:24633800-24640200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:24634200-24640000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:24634400-24636800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:24634600-24636600	Weak transcription	Fetal Intestine Small	intestine
14	chr3:24634600-24637000	Weak transcription	NHEK	skin
15	chr3:24634600-24637200	Weak transcription	Fetal Intestine Large	intestine
16	chr3:24634600-24637200	Weak transcription	Hela-S3	cervix
17	chr3:24635400-24637600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:24635600-24641400	Enhancers	HMEC	breast
19	chr3:24635800-24637200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:24636000-24637000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:24636000-24640000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:24636000-24640200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:24636200-24637800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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