Variant report

Variant	rs2839007
Chromosome Location	chr21:47241864-47241865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47239959..47242449-chr21:47264107..47266678,2	K562	blood:
2	chr21:46961760..46964733-chr21:47240674..47242196,2	MCF-7	breast:
3	chr21:46973106..46978237-chr21:47237804..47242212,8	MCF-7	breast:
4	chr21:46901426..46903468-chr21:47240521..47242930,2	K562	blood:
5	chr21:47062419..47066562-chr21:47239039..47241901,3	MCF-7	breast:
6	chr21:46973481..46977035-chr21:47238682..47244036,11	MCF-7	breast:
7	chr21:46960029..46961702-chr21:47241854..47244149,2	K562	blood:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction
ENSG00000173638	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11089022	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11089023	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11702443	0.84[ASN][1000 genomes]
rs11702478	0.85[ASN][1000 genomes]
rs11702552	0.84[ASN][1000 genomes]
rs1556335	1.00[YRI][hapmap]
rs2075885	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2150452	1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839006	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839012	0.88[ASN][1000 genomes]
rs2839015	0.93[ASN][1000 genomes]
rs2839016	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2839027	0.87[ASN][1000 genomes]
rs2839028	0.87[ASN][1000 genomes]
rs2839034	0.84[ASN][1000 genomes]
rs3788219	0.86[ASN][1000 genomes]
rs4819150	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61496907	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7276396	0.84[ASN][1000 genomes]
rs7281669	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs741955	0.86[ASN][1000 genomes]
rs743352	0.84[ASN][1000 genomes]
rs8129118	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8129304	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9306138	0.91[YRI][hapmap]
rs971977	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9979633	1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
2	chr21:47236400-47243800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:47239400-47247200	Weak transcription	Primary T cells from cord blood	blood
4	chr21:47240200-47243600	Enhancers	Liver	Liver
5	chr21:47240400-47242400	Enhancers	Fetal Heart	heart
6	chr21:47240600-47256600	Weak transcription	Dnd41	blood
7	chr21:47240800-47242200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr21:47240800-47242600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:47240800-47242600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr21:47240800-47244800	Weak transcription	Thymus	Thymus
11	chr21:47241000-47242000	Weak transcription	Spleen	Spleen
12	chr21:47241000-47242600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:47241000-47243200	Weak transcription	HSMM	muscle
14	chr21:47241000-47251800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:47241000-47255400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr21:47241200-47250200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:47241400-47249600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr21:47241600-47242000	Bivalent Enhancer	HMEC	breast
19	chr21:47241600-47242600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:47241600-47257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr21:47241800-47242200	Bivalent Enhancer	NHEK	skin
22	chr21:47241800-47246200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr21:47241800-47246400	Weak transcription	Fetal Thymus	thymus
24	chr21:47241800-47257600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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