Variant report

Variant	rs2838988
Chromosome Location	chr21:47156042-47156043
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47155045..47157882-chr21:47165789..47168073,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1029014	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089024	0.92[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs12151963	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12381207	0.85[ASN][1000 genomes]
rs12481867	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12481913	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12482094	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs12482377	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482750	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12482853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12483018	0.82[EUR][1000 genomes]
rs12483701	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051489	0.80[ASN][1000 genomes]
rs1467758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17004799	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351433	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1964928	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989537	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2065334	1.00[JPT][hapmap]
rs2150460	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2183596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2183601	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838978	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838981	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838983	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838985	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838990	0.86[ASN][1000 genomes]
rs2838991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2838992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs2838993	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838994	0.87[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs2838995	0.84[ASN][1000 genomes]
rs2839004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839005	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2839009	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2839013	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2839014	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2839026	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839029	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839032	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28583990	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28625750	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28692915	0.80[EUR][1000 genomes]
rs3367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[ASN][1000 genomes]
rs3788211	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788216	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3788220	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788224	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3788227	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3920695	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4347938	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4434082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818795	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818797	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818798	0.83[ASN][1000 genomes]
rs4818801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819134	0.85[ASN][1000 genomes]
rs4819144	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819156	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4819157	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs55707606	0.84[ASN][1000 genomes]
rs55912508	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923134	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55957843	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56012600	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56213918	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56288252	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56300316	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56323347	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56378934	0.84[ASN][1000 genomes]
rs57057834	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57282159	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57328058	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57501220	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57990579	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58368336	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58925015	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60604183	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60988006	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61100346	0.84[ASN][1000 genomes]
rs61329313	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61540945	0.85[ASN][1000 genomes]
rs62213277	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215031	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215035	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215040	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62215047	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215048	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62216072	0.85[ASN][1000 genomes]
rs62216073	0.83[ASN][1000 genomes]
rs66552772	0.84[ASN][1000 genomes]
rs67222545	0.85[ASN][1000 genomes]
rs67565220	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs725358	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276632	0.82[ASN][1000 genomes]
rs7279909	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280055	0.85[ASN][1000 genomes]
rs7280560	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283803	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7410008	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs744506	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs767137	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8127428	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs8133966	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882669	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs914241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9306139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637169	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637205	0.84[ASN][1000 genomes]
rs9637206	0.84[ASN][1000 genomes]
rs9637208	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs9647229	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647230	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs9974491	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9975404	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976200	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9976878	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9977309	0.84[ASN][1000 genomes]
rs9977908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9978078	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9978158	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9978882	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9981586	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2838988	PCBP3	cis	lung	GTEx
rs2838988	PCBP3	cis	cerebellum	SCAN
rs2838988	COL6A1	cis	parietal	SCAN
rs2838988	TRPM2	cis	cerebellum	SCAN
rs2838988	PCBP3	cis	Muscle Skeletal	GTEx
rs2838988	COL6A1	cis	cerebellum	SCAN

Chromatin state (count:19 , 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	chr21:47144600-47157600	Weak transcription	Right Atrium	heart
4	chr21:47145400-47156200	Weak transcription	Brain Substantia Nigra	brain
5	chr21:47146600-47159600	Weak transcription	Spleen	Spleen
6	chr21:47146600-47160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:47151800-47164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr21:47152600-47157600	Strong transcription	Fetal Thymus	thymus
9	chr21:47152600-47160400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr21:47153200-47165400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr21:47154000-47156600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr21:47154400-47158000	Strong transcription	Thymus	Thymus
13	chr21:47154400-47160000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:47154800-47156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:47155200-47156200	Enhancers	Fetal Heart	heart
16	chr21:47155200-47158600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr21:47155400-47156400	Enhancers	Right Ventricle	heart
18	chr21:47155400-47156800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr21:47156000-47156200	Enhancers	Brain Hippocampus Middle	brain

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