Variant report

Variant	rs9981017
Chromosome Location	chr21:28221615-28221616
allele	A/G
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	SMC3	chr21:28221486-28223720	SK-N-SH	brain:	n/a	chr21:28222531-28222539 chr21:28222531-28222545 chr21:28221938-28221952
2	CTCF	chr21:28221540-28221690	RPTEC	kidney:	n/a	n/a
3	CTCF	chr21:28221385-28223426	SK-N-SH	brain:	n/a	chr21:28221936-28221954 chr21:28222530-28222546 chr21:28222529-28222547 chr21:28222532-28222541 chr21:28222531-28222552 chr21:28221937-28221953 chr21:28221938-28221959
4	RAD21	chr21:28221130-28224365	SK-N-SH	brain:	n/a	chr21:28221937-28221956 chr21:28222530-28222549 chr21:28222531-28222540
5	RFX5	chr21:28221328-28223492	SK-N-SH	brain:	n/a	chr21:28222475-28222489 chr21:28222477-28222486 chr21:28222474-28222489
6	CTCF	chr21:28221579-28221693	K562	blood:	n/a	n/a
7	RAD21	chr21:28221585-28223693	IMR90	lung:	n/a	chr21:28221937-28221956 chr21:28222530-28222549 chr21:28222531-28222540

No.	Distal block	Cell Line	Cell type
1	chr21:28221411..28222029-chr21:29073057..29074050,3	K562	blood:
2	chr21:28221480..28222424-chr21:29708332..29709133,2	MCF-7	breast:
3	chr21:28141934..28142596-chr21:28221483..28222068,2	MCF-7	breast:
4	chr21:28221458..28223181-chr21:30117045..30118660,24	K562	blood:
5	chr21:28221528..28223154-chr21:29072525..29074611,26	MCF-7	breast:
6	chr21:28221585..28222726-chr21:29073735..29074729,3	MCF-7	breast:
7	chr21:28221528..28222669-chr21:29423576..29424576,3	MCF-7	breast:

Variant related genes	Relation type
ADAMTS1	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10460698	0.91[ASN][1000 genomes]
rs10470139	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11910373	0.91[ASN][1000 genomes]
rs1444274	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1475583	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1475584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2830553	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2830557	0.83[ASN][1000 genomes]
rs67979457	0.91[ASN][1000 genomes]
rs9305292	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9305293	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9976037	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9976082	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9981095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9981427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv3482	chr21:28191297-28221975	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28219200-28223000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:28219400-28223400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr21:28219400-28224800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:28219400-28229000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr21:28219600-28222000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr21:28219600-28222000	Weak transcription	Liver	Liver
7	chr21:28219600-28222200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr21:28219600-28223000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr21:28219600-28223200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:28219600-28223400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:28219600-28223400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:28219600-28223400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr21:28219600-28223400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr21:28219800-28222000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:28219800-28222000	Enhancers	Brain Hippocampus Middle	brain
16	chr21:28219800-28222000	Weak transcription	Osteobl	bone
17	chr21:28219800-28222600	Weak transcription	Fetal Kidney	kidney
18	chr21:28219800-28223600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr21:28220000-28222200	Weak transcription	Fetal Intestine Large	intestine
20	chr21:28220000-28222200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr21:28220000-28222400	Enhancers	Dnd41	blood
22	chr21:28220200-28223000	Weak transcription	Brain Substantia Nigra	brain
23	chr21:28220200-28223400	Weak transcription	Brain Angular Gyrus	brain
24	chr21:28220600-28222800	Weak transcription	Fetal Stomach	stomach
25	chr21:28220600-28223200	Weak transcription	Brain Anterior Caudate	brain
26	chr21:28221200-28221800	Enhancers	Brain Cingulate Gyrus	brain
27	chr21:28221400-28223000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr21:28221400-28223200	Enhancers	Fetal Lung	lung
29	chr21:28221600-28221800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr21:28221600-28221800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
31	chr21:28221600-28221800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr21:28221600-28221800	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr21:28221600-28221800	Enhancers	Fetal Intestine Small	intestine
34	chr21:28221600-28221800	Enhancers	Rectal Smooth Muscle	rectum
35	chr21:28221600-28221800	Enhancers	NH-A	brain
36	chr21:28221600-28221800	Enhancers	NHLF	lung
37	chr21:28221600-28222200	Enhancers	NHDF-Ad	bronchial
38	chr21:28221600-28222400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:28221600-28222400	Enhancers	Colon Smooth Muscle	Colon
40	chr21:28221600-28222400	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr21:28221600-28222400	Enhancers	Hela-S3	cervix
42	chr21:28221600-28222400	Enhancers	HSMM	muscle
43	chr21:28221600-28223000	Enhancers	Muscle Satellite Cultured Cells	--

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