Variant report

Variant	rs964975
Chromosome Location	chr21:47259576-47259577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr21:47259239-47259582	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr21:47259183-47259584	MCF10A-Er-Src	breast:	n/a	n/a
3	TCF12	chr21:47259095-47259654	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr21:47259137-47259727	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr21:47259122-47259704	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr21:47259079-47259645	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr21:47259120-47259596	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47257190..47260005-chr21:47265923..47268414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205424	TF binding region
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1014446	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10854472	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089024	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481867	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481913	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12481970	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12481977	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482010	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12482094	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482377	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482750	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12482853	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1467758	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17351419	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351433	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065334	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2183595	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2183596	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2838973	0.92[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2838974	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838976	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838982	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838989	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2838991	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838992	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2838993	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838994	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2838999	0.82[ASN][1000 genomes]
rs2839000	0.82[ASN][1000 genomes]
rs2839001	0.82[ASN][1000 genomes]
rs2839002	0.82[ASN][1000 genomes]
rs2839003	0.87[ASN][1000 genomes]
rs2839004	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2839005	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2839009	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs2839013	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2839014	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839026	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839029	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2839032	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3367	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs3788208	0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788209	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788211	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788215	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788216	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3788224	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3788227	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920695	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs4434082	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs4818801	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4818802	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818803	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818805	0.96[ASN][1000 genomes]
rs4819151	0.82[ASN][1000 genomes]
rs4819152	0.82[ASN][1000 genomes]
rs4819154	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819155	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819156	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819157	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780126	0.87[ASN][1000 genomes]
rs55856400	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55875620	0.87[ASN][1000 genomes]
rs55912352	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55927540	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs55996718	0.84[EUR][1000 genomes]
rs56256701	0.81[ASN][1000 genomes]
rs57688476	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58952758	0.82[ASN][1000 genomes]
rs59785950	0.82[ASN][1000 genomes]
rs61063225	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61276251	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62211883	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211885	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211886	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211895	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211925	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211926	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214592	0.82[ASN][1000 genomes]
rs62214596	0.82[ASN][1000 genomes]
rs62214597	0.82[ASN][1000 genomes]
rs62214599	0.82[ASN][1000 genomes]
rs62214604	0.87[ASN][1000 genomes]
rs62214608	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66523344	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66991496	0.82[ASN][1000 genomes]
rs67055992	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67878041	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280173	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127369	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8127428	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882668	0.94[ASN][1000 genomes]
rs882669	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs914241	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs9306139	0.93[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs9637208	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977908	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9978740	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9983770	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs964975	PCBP3	cis	cerebellum	SCAN
rs964975	COL18A1	cis	parietal	SCAN
rs964975	TRPM2	cis	cerebellum	SCAN
rs964975	PCBP3	cis	Muscle Skeletal	GTEx
rs964975	COL6A1	cis	parietal	SCAN
rs964975	PCBP3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
2	chr21:47255200-47259800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr21:47256600-47260600	Weak transcription	Fetal Brain Male	brain
4	chr21:47257200-47259800	Enhancers	NH-A	brain
5	chr21:47257200-47260800	Weak transcription	Fetal Kidney	kidney
6	chr21:47257400-47260400	Weak transcription	Primary T cells from cord blood	blood
7	chr21:47257800-47259600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr21:47257800-47259600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr21:47257800-47260400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:47257800-47260600	Weak transcription	Thymus	Thymus
11	chr21:47258000-47259800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr21:47258200-47259800	Enhancers	HSMM	muscle
13	chr21:47258600-47259600	Enhancers	NHDF-Ad	bronchial
14	chr21:47258600-47259800	Enhancers	NHEK	skin
15	chr21:47258800-47259600	Enhancers	Osteobl	bone
16	chr21:47259000-47259800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr21:47259200-47259600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr21:47259200-47259600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr21:47259200-47259600	Enhancers	HSMMtube	muscle
20	chr21:47259200-47259800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr21:47259200-47259800	Enhancers	HMEC	breast
22	chr21:47259400-47259600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr21:47259400-47259800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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