Variant report

Variant	rs12626782
Chromosome Location	chr21:47468937-47468938
allele	A/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	ZBTB7A	chr21:47468829-47470855	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr21:47468762-47470829	ECC-1	luminal epithelium:	n/a	chr21:47469229-47469236 chr21:47469696-47469703
3	POLR2A	chr21:47468879-47469830	U87	brain:	n/a	n/a
4	EP300	chr21:47468774-47470901	ECC-1	luminal epithelium:	n/a	chr21:47469020-47469033 chr21:47469509-47469516 chr21:47469720-47469729
5	NFIC	chr21:47468818-47470859	ECC-1	luminal epithelium:	n/a	n/a
6	MAZ	chr21:47468629-47470269	IMR90	lung:	n/a	chr21:47469643-47469659
7	POLR2A	chr21:47468296-47473687	IMR90	lung:	n/a	n/a
8	ESR1	chr21:47468935-47470524	ECC-1	luminal epithelium:	n/a	n/a
9	RCOR1	chr21:47468799-47470288	IMR90	lung:	n/a	n/a
10	FOXM1	chr21:47468907-47470683	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr21:47468873-47469830	U87	brain:	n/a	n/a
12	ZBTB7A	chr21:47468858-47471193	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr21:47468932-47470746	ECC-1	luminal epithelium:	n/a	chr21:47469020-47469033 chr21:47469509-47469516 chr21:47469720-47469729
14	CTCF	chr21:47468880-47469030	NHDF-neo	bronchial:	n/a	n/a
15	RAD21	chr21:47468837-47470560	ECC-1	luminal epithelium:	n/a	chr21:47469066-47469076
16	NFIC	chr21:47468848-47470779	ECC-1	luminal epithelium:	n/a	n/a
17	MAX	chr21:47468896-47470701	ECC-1	luminal epithelium:	n/a	chr21:47469643-47469659

No.	Distal block	Cell Line	Cell type
1	chr21:47464638..47467897-chr21:47467945..47470124,3	K562	blood:
2	chr21:47464638..47466951-chr21:47467945..47470531,2	K562	blood:
3	chr21:47467167..47469249-chr21:47470137..47471990,2	K562	blood:

Variant related genes	Relation type
ENSG00000228235	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11089041	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13048668	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13051123	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839089	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839091	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35458561	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35743884	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35780078	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4490283	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4819185	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4819186	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67011522	0.91[EUR][1000 genomes]
rs67017615	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67620707	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68050354	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72613654	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73159633	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9798612	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
11	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
12	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
13	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
14	nsv914091	chr21:47383056-47483799	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
15	esv1802000	chr21:47394780-47476081	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
16	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
17	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
18	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
19	nsv459310	chr21:47409503-47488387	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
20	nsv587935	chr21:47409503-47488387	Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
21	nsv1062861	chr21:47434057-47568806	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
22	nsv531548	chr21:47439416-47516220	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
23	nsv914097	chr21:47445791-47505084	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
24	nsv914098	chr21:47467894-47619784	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 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	chr21:47467000-47469000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:47468000-47472600	Enhancers	Fetal Lung	lung
3	chr21:47468200-47469000	Enhancers	Placenta	Placenta
4	chr21:47468200-47470400	Enhancers	Colonic Mucosa	Colon
5	chr21:47468200-47470400	Enhancers	Fetal Stomach	stomach
6	chr21:47468200-47471600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr21:47468200-47477800	Enhancers	NHDF-Ad	bronchial
8	chr21:47468200-47478000	Enhancers	Fetal Muscle Leg	muscle
9	chr21:47468400-47469600	Enhancers	Osteobl	bone
10	chr21:47468400-47470600	Enhancers	NHLF	lung
11	chr21:47468400-47473000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr21:47468600-47469000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr21:47468600-47469000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr21:47468600-47470200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr21:47468600-47470400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr21:47468600-47470400	Enhancers	Rectal Smooth Muscle	rectum
17	chr21:47468600-47470400	Enhancers	HSMMtube	muscle
18	chr21:47468800-47469000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr21:47468800-47469000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr21:47468800-47469000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:47468800-47469000	Enhancers	Fetal Intestine Large	intestine
22	chr21:47468800-47469200	Flanking Active TSS	HSMM	muscle
23	chr21:47468800-47469600	Enhancers	Fetal Intestine Small	intestine
24	chr21:47468800-47470000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr21:47468800-47470000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr21:47468800-47470000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr21:47468800-47470000	Enhancers	Fetal Muscle Trunk	muscle
28	chr21:47468800-47470400	Enhancers	Colon Smooth Muscle	Colon
29	chr21:47468800-47470400	Enhancers	Right Atrium	heart
30	chr21:47468800-47470400	Enhancers	HMEC	breast
31	chr21:47468800-47470400	Enhancers	NH-A	brain
32	chr21:47468800-47470600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr21:47468800-47470800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr21:47468800-47470800	Enhancers	Adipose Nuclei	Adipose
35	chr21:47468800-47471000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr21:47468800-47471000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
37	chr21:47468800-47471200	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links