Variant report

Variant	rs743479
Chromosome Location	chr21:45611950-45611951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45605212..45608621-chr21:45608817..45614047,5	K562	blood:
2	chr21:45610715..45617377-chr21:45717031..45721978,7	MCF-7	breast:
3	chr21:45610680..45613679-chr21:45657014..45661776,5	MCF-7	breast:
4	chr21:45610778..45612309-chr21:45667999..45669878,2	MCF-7	breast:
5	chr21:45611519..45615384-chr21:45659181..45663993,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160223	Chromatin interaction
ENSG00000141959	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11089118	0.82[EUR][1000 genomes]
rs2070551	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070552	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838516	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838519	0.96[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2838520	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838521	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2876932	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35405602	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3746958	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3804031	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804032	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4317019	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4380337	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4456788	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4635612	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7276302	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7280525	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7282490	0.93[CEU][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs743478	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762421	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762422	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762423	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8127691	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130872	1.00[YRI][hapmap]
rs8134436	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
12	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
13	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv913899	chr21:45577102-45611950	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	esv3411301	chr21:45609579-45620771	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv3455479	chr21:45609616-45620726	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	esv3455480	chr21:45609633-45620722	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs743479	KRTAP10-3	cis	cerebellum	SCAN
rs743479	WRB	cis	cerebellum	SCAN
rs743479	C21orf2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45602800-45612200	Weak transcription	Right Atrium	heart
2	chr21:45605400-45612200	Weak transcription	Left Ventricle	heart
3	chr21:45605400-45613800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr21:45606000-45613800	Weak transcription	Stomach Mucosa	stomach
5	chr21:45608600-45612000	Weak transcription	Esophagus	oesophagus
6	chr21:45608600-45612400	Weak transcription	Ovary	ovary
7	chr21:45610200-45614800	Enhancers	NHLF	lung
8	chr21:45610400-45615000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:45610400-45615400	Enhancers	NHDF-Ad	bronchial
10	chr21:45610400-45616000	Weak transcription	Thymus	Thymus
11	chr21:45610600-45612200	ZNF genes & repeats	Fetal Muscle Leg	muscle
12	chr21:45610800-45612000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr21:45610800-45612600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr21:45610800-45612800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:45610800-45616600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr21:45610800-45617600	Enhancers	Placenta	Placenta
17	chr21:45611000-45612000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr21:45611200-45612000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:45611200-45612200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr21:45611200-45612200	Weak transcription	Lung	lung
21	chr21:45611200-45612200	Weak transcription	Spleen	Spleen
22	chr21:45611200-45612400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr21:45611200-45613600	Weak transcription	Pancreas	Pancrea
24	chr21:45611200-45614800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr21:45611200-45616200	Weak transcription	Gastric	stomach
26	chr21:45611400-45612400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr21:45611400-45612600	Enhancers	Right Ventricle	heart
28	chr21:45611400-45614800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr21:45611600-45613000	Enhancers	Brain Cingulate Gyrus	brain
30	chr21:45611600-45614600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr21:45611600-45615200	Enhancers	Colon Smooth Muscle	Colon
32	chr21:45611600-45615400	Enhancers	Brain Anterior Caudate	brain
33	chr21:45611800-45612200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr21:45611800-45612200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr21:45611800-45612800	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr21:45611800-45612800	Enhancers	Brain Angular Gyrus	brain
37	chr21:45611800-45613000	Enhancers	Colonic Mucosa	Colon
38	chr21:45611800-45613200	Enhancers	HSMMtube	muscle
39	chr21:45611800-45615000	Enhancers	Brain Hippocampus Middle	brain
40	chr21:45611800-45615000	Enhancers	Brain Substantia Nigra	brain

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