Variant report

Variant	rs743476
Chromosome Location	chr21:45610369-45610370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45609994..45611618-chr21:45719686..45721405,2	MCF-7	breast:
2	chr21:45605212..45608621-chr21:45608817..45614047,5	K562	blood:
3	chr21:45609075..45610927-chr21:45615037..45616803,2	K562	blood:
4	chr21:45604879..45610592-chr21:45658595..45664052,16	MCF-7	breast:
5	chr21:45610065..45610976-chr21:45717590..45718626,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ICOSLG-3	chr21:45610322-45610610	XLOC_014113

No data

Variant related genes	Relation type
ENSG00000141959	Chromatin interaction
ENSG00000160223	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2032325	0.95[ASN][1000 genomes]
rs2032326	0.95[ASN][1000 genomes]
rs2032327	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2032328	0.95[ASN][1000 genomes]
rs6518349	0.86[YRI][hapmap]
rs7283479	0.95[ASN][1000 genomes]
rs743477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762417	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762418	0.82[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs762419	0.88[EUR][1000 genomes]
rs8129605	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs874017	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9976849	0.88[CEU][hapmap];0.92[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs743476	SH3BGR	cis	cerebellum	SCAN
rs743476	KRTAP10-2	cis	cerebellum	SCAN
rs743476	AGPAT3	cis	parietal	SCAN
rs743476	KRTAP10-2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45602800-45612200	Weak transcription	Right Atrium	heart
2	chr21:45605200-45610800	Weak transcription	Right Ventricle	heart
3	chr21:45605400-45610800	Weak transcription	Pancreas	Pancrea
4	chr21:45605400-45610800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr21:45605400-45612200	Weak transcription	Left Ventricle	heart
6	chr21:45605400-45613800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr21:45605600-45610600	Weak transcription	Brain Substantia Nigra	brain
8	chr21:45605800-45611400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr21:45606000-45610600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr21:45606000-45610800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:45606000-45613800	Weak transcription	Stomach Mucosa	stomach
12	chr21:45606200-45610800	Weak transcription	Spleen	Spleen
13	chr21:45606400-45610800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr21:45606600-45610600	Weak transcription	Fetal Muscle Leg	muscle
15	chr21:45606800-45610800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:45608600-45610400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:45608600-45610400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:45608600-45611000	Weak transcription	Gastric	stomach
19	chr21:45608600-45612000	Weak transcription	Esophagus	oesophagus
20	chr21:45608600-45612400	Weak transcription	Ovary	ovary
21	chr21:45608800-45610800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr21:45609800-45610600	Enhancers	Fetal Muscle Trunk	muscle
23	chr21:45610200-45610400	Flanking Active TSS	NHDF-Ad	bronchial
24	chr21:45610200-45610600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr21:45610200-45610800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:45610200-45611000	Enhancers	Fetal Stomach	stomach
27	chr21:45610200-45611000	Enhancers	HepG2	liver
28	chr21:45610200-45614800	Enhancers	NHLF	lung

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