Variant report

Variant	rs8129304
Chromosome Location	chr21:47168775-47168776
allele	G/T
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	USF1	chr21:47168555-47168990	ECC-1	luminal epithelium:	n/a	chr21:47168791-47168802
2	USF2	chr21:47168637-47168917	Hela-S3	cervix:	n/a	chr21:47168791-47168802
3	MXI1	chr21:47166882-47168974	SK-N-SH	brain:	n/a	n/a
4	ELF1	chr21:47168512-47168953	MCF-7	breast:	n/a	n/a
5	USF1	chr21:47168696-47168889	HepG2	liver:	n/a	chr21:47168791-47168802
6	USF1	chr21:47168668-47168877	HepG2	liver:	n/a	chr21:47168791-47168802
7	JUND	chr21:47167154-47168911	SK-N-SH	brain:	n/a	chr21:47167897-47167905 chr21:47167895-47167907 chr21:47167897-47167904 chr21:47167897-47167906 chr21:47167896-47167906 chr21:47167895-47167906 chr21:47167896-47167905
8	USF2	chr21:47168673-47168925	HepG2	liver:	n/a	chr21:47168791-47168802
9	USF1	chr21:47168633-47168942	K562	blood:	n/a	chr21:47168791-47168802
10	USF1	chr21:47168608-47168971	ECC-1	luminal epithelium:	n/a	chr21:47168791-47168802

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47061926..47064777-chr21:47168199..47170677,2	MCF-7	breast:

Variant related genes	Relation type
PCBP3	TF binding region
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11089022	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11702443	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11702478	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11702850	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11911839	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12373907	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12627257	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1556335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2075885	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2150452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297293	0.83[ASN][1000 genomes]
rs2330245	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838972	0.81[ASN][1000 genomes]
rs2838984	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2839007	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2839015	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2839027	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2839028	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2839034	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs28438591	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3788219	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4818794	0.80[EUR][1000 genomes]
rs4819145	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4819146	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4819150	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62213280	0.85[ASN][1000 genomes]
rs7278438	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7281669	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743352	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs8128559	0.81[EUR][1000 genomes]
rs8129118	0.83[EUR][1000 genomes]
rs8134872	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs914243	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs9306138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9306141	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs971977	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9977795	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9978181	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9979633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[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	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
9	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
10	esv3438685	chr21:47163624-47168822	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47158800-47169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr21:47165000-47169000	Strong transcription	Primary T cells from cord blood	blood
3	chr21:47165800-47171000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr21:47166000-47171400	Weak transcription	Gastric	stomach
5	chr21:47166200-47174400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr21:47166200-47176800	Weak transcription	Dnd41	blood
7	chr21:47166200-47194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr21:47167200-47169000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr21:47167200-47169400	Enhancers	Fetal Muscle Leg	muscle
10	chr21:47167200-47169400	Strong transcription	Thymus	Thymus
11	chr21:47167400-47170000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr21:47167600-47168800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr21:47167600-47170200	Genic enhancers	Fetal Thymus	thymus
14	chr21:47167800-47176200	Weak transcription	NH-A	brain
15	chr21:47168000-47168800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr21:47168000-47170600	Weak transcription	Fetal Brain Female	brain
17	chr21:47168200-47168800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:47168200-47169000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr21:47168200-47169200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr21:47168200-47169800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:47168200-47170200	Strong transcription	Spleen	Spleen
22	chr21:47168400-47168800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:47168400-47168800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr21:47168400-47169200	Enhancers	HSMMtube	muscle
25	chr21:47168400-47169400	Enhancers	HSMM	muscle
26	chr21:47168400-47171800	Weak transcription	Adipose Nuclei	Adipose
27	chr21:47168400-47172000	Weak transcription	Brain Anterior Caudate	brain
28	chr21:47168400-47172400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr21:47168600-47168800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr21:47168600-47168800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr21:47168600-47170600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr21:47168600-47187000	Weak transcription	NHDF-Ad	bronchial

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