Variant report

Variant	rs17833407
Chromosome Location	chr9:21748320-21748321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21747038..21749658-chr9:21801876..21803848,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264545	Chromatin interaction
ENSG00000099810	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10118262	0.88[ASN][1000 genomes]
rs10119658	0.88[ASN][1000 genomes]
rs10738596	0.97[ASN][1000 genomes]
rs10738597	0.87[ASN][1000 genomes]
rs10738599	0.83[ASN][1000 genomes]
rs10757236	0.84[ASN][1000 genomes]
rs10757238	0.86[ASN][1000 genomes]
rs10757239	0.86[ASN][1000 genomes]
rs10757240	0.86[ASN][1000 genomes]
rs10757241	0.86[ASN][1000 genomes]
rs10757242	0.87[ASN][1000 genomes]
rs10757245	0.87[ASN][1000 genomes]
rs10757246	0.87[ASN][1000 genomes]
rs10757247	0.87[ASN][1000 genomes]
rs10757250	0.87[ASN][1000 genomes]
rs10757251	0.89[ASN][1000 genomes]
rs10757252	0.87[ASN][1000 genomes]
rs10757253	0.83[ASN][1000 genomes]
rs10757254	0.83[ASN][1000 genomes]
rs10757255	0.83[ASN][1000 genomes]
rs10811592	0.84[ASN][1000 genomes]
rs10811595	0.84[ASN][1000 genomes]
rs10811600	0.86[ASN][1000 genomes]
rs10811601	0.86[ASN][1000 genomes]
rs10811602	0.86[ASN][1000 genomes]
rs10811604	0.87[ASN][1000 genomes]
rs10811605	0.87[ASN][1000 genomes]
rs10811613	0.83[ASN][1000 genomes]
rs10965122	0.83[ASN][1000 genomes]
rs10965127	0.80[ASN][1000 genomes]
rs1335502	0.86[ASN][1000 genomes]
rs1335505	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs1335506	0.90[ASN][1000 genomes]
rs1335507	0.90[ASN][1000 genomes]
rs1335508	0.90[ASN][1000 genomes]
rs1335512	0.86[ASN][1000 genomes]
rs1345026	0.96[ASN][1000 genomes]
rs1345027	0.90[ASN][1000 genomes]
rs1372057	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs1372058	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs1372059	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs1414228	0.83[ASN][1000 genomes]
rs1414229	0.83[ASN][1000 genomes]
rs1414236	0.85[ASN][1000 genomes]
rs1414237	0.86[ASN][1000 genomes]
rs1414238	0.86[ASN][1000 genomes]
rs1414242	0.94[CHB][hapmap];0.91[CHD][hapmap];0.90[ASN][1000 genomes]
rs1414244	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs1414245	0.90[ASN][1000 genomes]
rs1414246	0.90[ASN][1000 genomes]
rs1414247	0.90[ASN][1000 genomes]
rs1414248	0.90[ASN][1000 genomes]
rs1414249	0.90[ASN][1000 genomes]
rs1414250	0.88[ASN][1000 genomes]
rs1414251	0.88[ASN][1000 genomes]
rs1414252	0.88[ASN][1000 genomes]
rs1414256	0.88[ASN][1000 genomes]
rs1414257	0.88[ASN][1000 genomes]
rs1440993	0.80[ASN][1000 genomes]
rs1542075	0.83[CHB][hapmap]
rs1542076	0.83[CHB][hapmap]
rs1932237	0.87[ASN][1000 genomes]
rs1965153	0.88[ASN][1000 genomes]
rs2027162	0.87[ASN][1000 genomes]
rs2027163	0.87[ASN][1000 genomes]
rs2043991	0.82[ASN][1000 genomes]
rs2119466	0.87[ASN][1000 genomes]
rs2119467	0.87[ASN][1000 genomes]
rs2152272	0.82[ASN][1000 genomes]
rs2152273	0.83[ASN][1000 genomes]
rs2165408	0.83[CHB][hapmap]
rs2165411	0.82[ASN][1000 genomes]
rs2184551	0.83[ASN][1000 genomes]
rs2218220	0.88[ASN][1000 genomes]
rs2891159	0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[ASN][1000 genomes]
rs2891160	0.86[ASN][1000 genomes]
rs3849929	0.83[ASN][1000 genomes]
rs3928894	0.83[CHB][hapmap]
rs4300088	0.88[ASN][1000 genomes]
rs4350062	0.86[ASN][1000 genomes]
rs4352937	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs4364717	0.83[CHB][hapmap]
rs4384075	0.84[ASN][1000 genomes]
rs4548267	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs4636294	0.89[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs62558566	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62559378	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6475554	0.84[ASN][1000 genomes]
rs6475555	0.84[ASN][1000 genomes]
rs6475564	0.82[ASN][1000 genomes]
rs6475566	0.86[ASN][1000 genomes]
rs6475568	0.86[ASN][1000 genomes]
rs6475569	0.86[ASN][1000 genomes]
rs6475571	0.84[ASN][1000 genomes]
rs6475572	0.84[ASN][1000 genomes]
rs6475574	0.84[ASN][1000 genomes]
rs6475576	0.84[ASN][1000 genomes]
rs6475578	0.83[ASN][1000 genomes]
rs6475579	0.83[ASN][1000 genomes]
rs6475585	0.86[CHB][hapmap]
rs7021012	0.81[ASN][1000 genomes]
rs7021538	0.86[ASN][1000 genomes]
rs7023299	0.82[ASN][1000 genomes]
rs7023474	0.83[CHB][hapmap]
rs7024027	0.83[ASN][1000 genomes]
rs7028913	0.84[ASN][1000 genomes]
rs7029040	0.84[ASN][1000 genomes]
rs7029166	0.84[ASN][1000 genomes]
rs7029274	0.84[ASN][1000 genomes]
rs7037577	0.82[ASN][1000 genomes]
rs7043827	0.82[ASN][1000 genomes]
rs7045768	0.83[ASN][1000 genomes]
rs7850446	0.84[ASN][1000 genomes]
rs7852710	0.88[ASN][1000 genomes]
rs7852900	0.87[ASN][1000 genomes]
rs7853131	0.87[ASN][1000 genomes]
rs7854018	0.86[ASN][1000 genomes]
rs7854222	0.85[ASN][1000 genomes]
rs7855242	0.82[ASN][1000 genomes]
rs7856941	0.84[ASN][1000 genomes]
rs7858991	0.86[ASN][1000 genomes]
rs7860576	0.84[ASN][1000 genomes]
rs7866540	0.84[ASN][1000 genomes]
rs7866787	0.85[ASN][1000 genomes]
rs7866885	0.84[ASN][1000 genomes]
rs7871345	0.82[ASN][1000 genomes]
rs7874319	0.86[ASN][1000 genomes]
rs869330	0.83[CHB][hapmap]
rs871024	0.83[CHB][hapmap]
rs9298823	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs9298824	0.90[ASN][1000 genomes]
rs9298825	0.90[ASN][1000 genomes]
rs9886831	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17833407	PLIN2	cis	parietal	SCAN
rs17833407	MTAP	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21743200-21750000	Weak transcription	NH-A	brain
2	chr9:21743400-21750000	Weak transcription	Osteobl	bone
3	chr9:21744200-21752200	Enhancers	HMEC	breast
4	chr9:21745000-21748800	Enhancers	NHEK	skin
5	chr9:21746600-21748600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:21746600-21748800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:21746600-21751200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:21746800-21748400	Enhancers	Hela-S3	cervix
9	chr9:21747000-21750000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:21747200-21752000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:21747600-21750000	Weak transcription	NHDF-Ad	bronchial
12	chr9:21747800-21749800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:21747800-21751800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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