Variant report

Variant	rs60988006
Chromosome Location	chr21:47054390-47054391
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	chr21:47044412..47047095-chr21:47051523..47054787,3	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1029014	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12151963	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12381207	0.98[ASN][1000 genomes]
rs12483018	0.85[EUR][1000 genomes]
rs12483701	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1467758	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17004799	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1964928	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1989537	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2150460	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2183595	0.83[ASN][1000 genomes]
rs2183596	0.83[ASN][1000 genomes]
rs2183601	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838973	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838974	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838976	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838978	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838981	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838982	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838983	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838985	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838988	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838990	0.83[ASN][1000 genomes]
rs2838991	0.83[ASN][1000 genomes]
rs2838992	0.83[ASN][1000 genomes]
rs2838993	0.83[ASN][1000 genomes]
rs2838994	0.81[ASN][1000 genomes]
rs2838995	0.81[ASN][1000 genomes]
rs28625750	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28692915	0.83[EUR][1000 genomes]
rs3367	0.83[ASN][1000 genomes]
rs3920695	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4347938	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4434082	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4818795	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4818797	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4819134	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819144	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55707606	0.81[ASN][1000 genomes]
rs55912508	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55923134	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55957843	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56213918	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56288252	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56300316	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56323347	0.83[ASN][1000 genomes]
rs56378934	0.81[ASN][1000 genomes]
rs57057834	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57282159	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57328058	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57501220	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57990579	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58368336	0.85[EUR][1000 genomes]
rs58925015	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60604183	0.83[ASN][1000 genomes]
rs61100346	0.81[ASN][1000 genomes]
rs61329313	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61540945	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62213277	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62215031	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62215035	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62215040	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62215047	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62215048	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62216072	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62216073	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66552772	0.81[ASN][1000 genomes]
rs67222545	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67565220	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs725358	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7279909	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7280055	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7280560	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7283803	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7410008	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744506	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767137	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8133966	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs914241	0.83[ASN][1000 genomes]
rs9306139	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9637169	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9637205	0.81[ASN][1000 genomes]
rs9637206	0.81[ASN][1000 genomes]
rs9647229	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9647230	0.83[ASN][1000 genomes]
rs9974491	0.83[ASN][1000 genomes]
rs9975404	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9976200	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9976878	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9977309	0.81[ASN][1000 genomes]
rs9978078	0.83[ASN][1000 genomes]
rs9978158	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9978882	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9981586	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2762114	chr21:46680202-47067744	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
5	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
6	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
7	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
8	nsv914077	chr21:46998548-47091361	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
10	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
11	esv3405686	chr21:47050724-47057922	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv3361506	chr21:47051224-47055822	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	esv3415750	chr21:47052324-47057922	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	esv994264	chr21:47052861-47054551	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
15	esv14982	chr21:47052971-47054551	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	n/a
16	esv14100	chr21:47053051-47056946	Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv587864	chr21:47053453-47070718	Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	esv3412278	chr21:47053724-47057822	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs60988006	PCBP3	cis	Muscle Skeletal	GTEx
rs60988006	PCBP3	cis	lung	GTEx
rs60988006	PCBP3	cis	Nerve Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47050400-47055800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:47052600-47059000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr21:47052800-47058000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr21:47052800-47058400	Weak transcription	Primary T cells from cord blood	blood
5	chr21:47053000-47058000	Weak transcription	Dnd41	blood
6	chr21:47053200-47054400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr21:47053200-47054600	Weak transcription	GM12878-XiMat	blood
8	chr21:47053200-47055400	Weak transcription	Esophagus	oesophagus
9	chr21:47053200-47055800	Weak transcription	Spleen	Spleen
10	chr21:47054200-47054600	Active TSS	Thymus	Thymus
11	chr21:47054200-47055000	Flanking Active TSS	Fetal Thymus	thymus

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