Variant report

Variant	rs13051682
Chromosome Location	chr21:47167040-47167041
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	SIX5	chr21:47166456-47167065	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:47165519-47167135	GM12892	blood:	n/a	n/a
3	BCL3	chr21:47166740-47167053	GM12878	blood:	n/a	n/a
4	MXI1	chr21:47166882-47168974	SK-N-SH	brain:	n/a	n/a
5	POU2F2	chr21:47165680-47167042	GM12891	blood:	n/a	n/a
6	TCF3	chr21:47165596-47167097	GM12878	blood:	n/a	n/a
7	POU2F2	chr21:47165679-47167041	GM12891	blood:	n/a	n/a
8	CTCF	chr21:47167005-47167044	LNCaP	prostate:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47163262..47166071-chr21:47166179..47167744,2	MCF-7	breast:
2	chr21:47155045..47157882-chr21:47165789..47168073,2	MCF-7	breast:

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13047397	1.00[AFR][1000 genomes]
rs13049610	1.00[AFR][1000 genomes]
rs13050195	1.00[AFR][1000 genomes]
rs2330186	1.00[AFR][1000 genomes]
rs34223052	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34288474	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34396939	1.00[AFR][1000 genomes]
rs34959654	1.00[AFR][1000 genomes]
rs35943749	1.00[AFR][1000 genomes]
rs4819131	1.00[AFR][1000 genomes]
rs4819132	1.00[AFR][1000 genomes]
rs6518255	1.00[AFR][1000 genomes]
rs71324442	1.00[AFR][1000 genomes]
rs71324443	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71324447	1.00[AFR][1000 genomes]
rs71324449	1.00[AFR][1000 genomes]
rs71324455	1.00[AFR][1000 genomes]
rs7276295	1.00[AFR][1000 genomes]
rs7282487	1.00[AFR][1000 genomes]
rs9637203	1.00[AFR][1000 genomes]
rs9637204	1.00[AFR][1000 genomes]
rs9984824	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1063957	chr21:47090475-47168291	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	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
10	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
11	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
12	esv3377547	chr21:47164324-47167922	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv3395748	chr21:47164324-47168022	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47144200-47167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr21:47156600-47168000	Weak transcription	Brain Angular Gyrus	brain
3	chr21:47157000-47168200	Weak transcription	Brain Hippocampus Middle	brain
4	chr21:47157800-47167400	Weak transcription	HSMMtube	muscle
5	chr21:47158800-47169800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr21:47159000-47168000	Weak transcription	Brain Anterior Caudate	brain
7	chr21:47162400-47167200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr21:47162400-47167200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr21:47162400-47167600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr21:47163000-47167400	Weak transcription	NHDF-Ad	bronchial
11	chr21:47164200-47167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:47164600-47168000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr21:47165000-47169000	Strong transcription	Primary T cells from cord blood	blood
14	chr21:47165600-47167600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr21:47165800-47167600	Strong transcription	Fetal Thymus	thymus
16	chr21:47165800-47171000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr21:47166000-47167200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:47166000-47167200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr21:47166000-47167400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr21:47166000-47167400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:47166000-47167600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr21:47166000-47167600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr21:47166000-47167600	Weak transcription	Adipose Nuclei	Adipose
24	chr21:47166000-47171400	Weak transcription	Gastric	stomach
25	chr21:47166200-47167200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr21:47166200-47167200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr21:47166200-47167200	Weak transcription	Thymus	Thymus
28	chr21:47166200-47167400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr21:47166200-47167400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr21:47166200-47167400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr21:47166200-47167400	Weak transcription	HSMM	muscle
32	chr21:47166200-47168200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:47166200-47168200	Weak transcription	Spleen	Spleen
34	chr21:47166200-47174400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr21:47166200-47176800	Weak transcription	Dnd41	blood
36	chr21:47166200-47194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr21:47167000-47167600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links