Variant report

Variant	rs525548
Chromosome Location	chr21:44780579-44780580
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	POLR2A	chr21:44779653-44782706	IMR90	lung:	n/a	n/a
2	MAZ	chr21:44780514-44782772	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:44779798..44782094-chr21:44814719..44816894,2	MCF-7	breast:
2	chr21:44779843..44781749-chr21:44914569..44917163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225637	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1000472	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1000474	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2073430	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs504285	0.90[MEX][hapmap]
rs504313	0.89[MEX][hapmap]
rs524850	0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs619484	1.00[MEX][hapmap]
rs633644	0.90[MEX][hapmap]
rs668058	0.95[MEX][hapmap]
rs681210	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
3	esv1817359	chr21:44699077-44821595	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	nsv1058308	chr21:44722915-44825108	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1063186	chr21:44729904-44828476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv544467	chr21:44729904-44828476	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv913837	chr21:44731138-44853859	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv913840	chr21:44750643-44823479	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913841	chr21:44761874-44853859	Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
14	nsv913842	chr21:44764895-44792929	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv913843	chr21:44774757-44810756	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv913844	chr21:44779680-44875495	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS 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	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs525548	NCRNA00257	cis	parietal	SCAN
rs525548	WRB	cis	cerebellum	SCAN
rs525548	C21orf29	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44754800-44781200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:44763600-44780800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr21:44768400-44781000	Weak transcription	Fetal Intestine Small	intestine
4	chr21:44769000-44780600	Weak transcription	Right Atrium	heart
5	chr21:44772400-44780800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr21:44772400-44781200	Enhancers	Fetal Muscle Leg	muscle
7	chr21:44774600-44780600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:44774800-44782000	Weak transcription	Brain Anterior Caudate	brain
9	chr21:44776600-44780600	Weak transcription	Fetal Heart	heart
10	chr21:44776600-44780800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:44776600-44780800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr21:44776600-44781000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr21:44776600-44781000	Weak transcription	Fetal Brain Female	brain
14	chr21:44777200-44782000	Enhancers	Brain Germinal Matrix	brain
15	chr21:44777400-44788600	Enhancers	Fetal Brain Male	brain
16	chr21:44778000-44781000	Enhancers	GM12878-XiMat	blood
17	chr21:44778200-44781200	Enhancers	Primary B cells from peripheral blood	blood
18	chr21:44778600-44781000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr21:44778800-44781400	Enhancers	Fetal Thymus	thymus
20	chr21:44779000-44781600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr21:44779200-44780800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr21:44779200-44780800	Enhancers	Fetal Muscle Trunk	muscle
23	chr21:44779200-44780800	Weak transcription	Psoas Muscle	Psoas
24	chr21:44779200-44781000	Weak transcription	Brain Angular Gyrus	brain
25	chr21:44779400-44780800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr21:44779400-44781400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr21:44779400-44782200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr21:44779600-44780800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr21:44779600-44780800	Weak transcription	Gastric	stomach
30	chr21:44779600-44781200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr21:44779600-44781200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr21:44779800-44780800	Enhancers	Dnd41	blood
33	chr21:44779800-44781200	Weak transcription	Brain Hippocampus Middle	brain
34	chr21:44780000-44781000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr21:44780000-44783600	Enhancers	Primary B cells from cord blood	blood
36	chr21:44780200-44780600	Weak transcription	Fetal Lung	lung
37	chr21:44780200-44780600	Bivalent Enhancer	Placenta	Placenta
38	chr21:44780200-44780800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr21:44780200-44781800	Enhancers	Left Ventricle	heart
40	chr21:44780200-44782000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr21:44780200-44782600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr21:44780200-44788400	Enhancers	Spleen	Spleen
43	chr21:44780400-44780800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr21:44780400-44781200	Enhancers	HMEC	breast
45	chr21:44780400-44781600	Enhancers	Lung	lung
46	chr21:44780400-44781600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr21:44780400-44782000	Enhancers	Esophagus	oesophagus

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