Variant report

Variant	rs56012600
Chromosome Location	chr21:47162487-47162488
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	chr21:47161212..47163794-chr21:47166078..47168615,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1029014	0.91[ASN][1000 genomes]
rs12151963	0.91[ASN][1000 genomes]
rs12329841	0.85[EUR][1000 genomes]
rs12329855	0.80[ASN][1000 genomes]
rs12482405	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12482648	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12482853	0.85[EUR][1000 genomes]
rs12483701	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13051489	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1467758	0.88[ASN][1000 genomes]
rs17004799	0.91[ASN][1000 genomes]
rs1964928	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1989537	0.86[ASN][1000 genomes]
rs2094888	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2150460	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2183595	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2183596	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2183601	0.86[ASN][1000 genomes]
rs2838973	0.88[ASN][1000 genomes]
rs2838974	0.88[ASN][1000 genomes]
rs2838976	0.88[ASN][1000 genomes]
rs2838978	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838981	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838982	0.91[ASN][1000 genomes]
rs2838983	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838985	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838988	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838989	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838990	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838991	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838992	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838993	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838994	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838995	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838996	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838997	0.86[ASN][1000 genomes]
rs2838998	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838999	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839000	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839001	0.82[ASN][1000 genomes]
rs2839002	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839003	0.85[EUR][1000 genomes]
rs2839004	0.82[EUR][1000 genomes]
rs2839005	0.84[EUR][1000 genomes]
rs2839009	0.85[EUR][1000 genomes]
rs28583990	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28625750	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3367	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920695	0.88[ASN][1000 genomes]
rs4347938	0.88[ASN][1000 genomes]
rs4434082	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4818795	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4818797	0.91[ASN][1000 genomes]
rs4818798	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4818801	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4819144	0.91[ASN][1000 genomes]
rs4819151	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4819152	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55707606	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55780126	0.84[EUR][1000 genomes]
rs55875620	0.84[EUR][1000 genomes]
rs55912508	0.91[ASN][1000 genomes]
rs55923134	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55957843	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56036552	0.84[EUR][1000 genomes]
rs56213918	0.86[ASN][1000 genomes]
rs56256701	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56288252	0.88[ASN][1000 genomes]
rs56300316	0.91[ASN][1000 genomes]
rs56323347	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56347571	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56378934	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57328058	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57501220	0.88[ASN][1000 genomes]
rs57990579	0.83[ASN][1000 genomes]
rs58925015	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58952758	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59398815	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59785950	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60604183	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61100346	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61329313	0.91[ASN][1000 genomes]
rs62213277	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62213555	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214592	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214596	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214597	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214599	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214604	0.85[EUR][1000 genomes]
rs62215031	0.88[ASN][1000 genomes]
rs62215035	0.88[ASN][1000 genomes]
rs62215040	0.88[ASN][1000 genomes]
rs62215047	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62215048	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs66552772	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66991496	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67565220	0.86[ASN][1000 genomes]
rs725358	0.91[ASN][1000 genomes]
rs7276632	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7279909	0.91[ASN][1000 genomes]
rs7280560	0.91[ASN][1000 genomes]
rs7283803	0.88[ASN][1000 genomes]
rs767137	0.91[ASN][1000 genomes]
rs8127369	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8127809	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8128722	0.80[ASN][1000 genomes]
rs8133966	0.91[ASN][1000 genomes]
rs914241	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9306139	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9637169	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9637205	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637206	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9647229	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9647230	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9974491	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9975404	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9976200	0.91[ASN][1000 genomes]
rs9976878	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9977309	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9977908	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9978078	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9978158	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9978740	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978882	0.88[ASN][1000 genomes]
rs9981586	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv1062702	chr21:47095762-47169369	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv544493	chr21:47095762-47169369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56012600	PCBP3	cis	Nerve Tibial	GTEx
rs56012600	PCBP3	cis	Muscle Skeletal	GTEx
rs56012600	PCBP3	cis	lung	GTEx
rs56012600	PCBP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47135600-47165000	Weak transcription	Primary T cells from cord blood	blood
2	chr21:47144200-47167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr21:47151800-47164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:47153200-47165400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr21:47156600-47168000	Weak transcription	Brain Angular Gyrus	brain
6	chr21:47156800-47164800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr21:47157000-47168200	Weak transcription	Brain Hippocampus Middle	brain
8	chr21:47157600-47165000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:47157800-47167400	Weak transcription	HSMMtube	muscle
10	chr21:47158000-47165400	Weak transcription	Dnd41	blood
11	chr21:47158800-47169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr21:47159000-47168000	Weak transcription	Brain Anterior Caudate	brain
13	chr21:47160000-47164800	Weak transcription	Thymus	Thymus
14	chr21:47160200-47164200	Weak transcription	Fetal Thymus	thymus
15	chr21:47160600-47165600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:47160600-47165600	Weak transcription	Gastric	stomach
17	chr21:47160800-47165800	Weak transcription	Adipose Nuclei	Adipose
18	chr21:47161200-47165000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr21:47161400-47164800	Weak transcription	Spleen	Spleen
20	chr21:47161400-47165400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr21:47161400-47165400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr21:47161400-47165600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr21:47161800-47162600	Enhancers	NHEK	skin
24	chr21:47162000-47164600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr21:47162400-47167200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr21:47162400-47167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr21:47162400-47167600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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