Variant report

Variant	rs2839026
Chromosome Location	chr21:47288665-47288666
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47283223..47285072-chr21:47288442..47290551,2	MCF-7	breast:
2	chr21:47288031..47288840-chr21:47325915..47326785,5	MCF-7	breast:
3	chr21:47286639..47289783-chr21:47334819..47337166,3	MCF-7	breast:
4	chr21:47237629..47240751-chr21:47286627..47289424,3	MCF-7	breast:
5	chr21:47280971..47284906-chr21:47285301..47288996,5	K562	blood:
6	chr21:47277116..47279764-chr21:47286679..47288942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1014446	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10854472	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089024	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12481970	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12481977	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482010	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12482094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12482853	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17351419	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065334	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2183595	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2183596	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838973	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2838974	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838976	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838982	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838989	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838991	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838992	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838993	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2838994	0.86[CHB][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	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2839005	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2839009	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2839013	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2839014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[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	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788208	0.85[CHB][hapmap];0.81[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788209	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788215	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3788224	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3788227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920695	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4434082	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4818801	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4818802	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818803	0.88[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	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819155	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780126	0.87[ASN][1000 genomes]
rs55856400	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55875620	0.87[ASN][1000 genomes]
rs55912352	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55927540	0.96[ASN][1000 genomes]
rs55996718	0.82[EUR][1000 genomes]
rs56256701	0.81[ASN][1000 genomes]
rs57688476	0.85[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	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61276251	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62211883	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211885	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211886	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211894	0.92[AFR][1000 genomes]
rs62211895	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211925	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211926	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[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	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66523344	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66991496	0.82[ASN][1000 genomes]
rs67055992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67878041	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280173	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127369	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8127428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882668	0.94[ASN][1000 genomes]
rs882669	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs914241	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9306139	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9637208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964975	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]
rs9977908	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9978740	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9983770	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
15	nsv914080	chr21:47265786-47311686	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS 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	2 gene(s)	inside rSNPs	n/a
16	nsv914081	chr21:47265786-47320805	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
19	nsv914084	chr21:47288453-47326666	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2839026	PCBP3	cis	lung	GTEx
rs2839026	PCBP3	cis	Muscle Skeletal	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47266800-47300600	Weak transcription	Right Atrium	heart
2	chr21:47273200-47289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr21:47273800-47299200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr21:47285600-47289400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr21:47285600-47289400	Weak transcription	NHDF-Ad	bronchial
6	chr21:47286000-47294000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:47286400-47289400	Weak transcription	HSMM	muscle
8	chr21:47286400-47289600	Weak transcription	HSMMtube	muscle
9	chr21:47286400-47294800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:47286600-47289200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr21:47286600-47289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:47286600-47289400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:47286600-47294800	Weak transcription	Fetal Thymus	thymus
14	chr21:47287000-47289400	Weak transcription	NH-A	brain
15	chr21:47287200-47289400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr21:47287400-47290400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr21:47287800-47288800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr21:47288000-47294800	Weak transcription	Thymus	Thymus
19	chr21:47288200-47292000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr21:47288400-47288800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr21:47288400-47288800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr21:47288400-47288800	Bivalent/Poised TSS	Osteobl	bone
23	chr21:47288400-47289600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr21:47288400-47289600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr21:47288600-47289400	Weak transcription	Spleen	Spleen
26	chr21:47288600-47292400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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