Variant report

Variant	rs17183473
Chromosome Location	chr21:47653345-47653346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:47650121-47657023	K562	blood:	n/a	n/a
2	POLR2A	chr21:47652647-47653410	K562	blood:	n/a	n/a
3	POLR2A	chr21:47653056-47653460	K562	blood:	n/a	n/a
4	POLR2A	chr21:47652675-47653438	K562	blood:	n/a	n/a
5	POLR2A	chr21:47653035-47653423	GM12891	blood:	n/a	n/a
6	POLR2A	chr21:47652658-47655345	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr21:47653227-47653915	U87	brain:	n/a	n/a
8	POLR2A	chr21:47652538-47653405	GM12892	blood:	n/a	n/a
9	POLR2A	chr21:47653313-47654500	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47646929..47655402-chr21:47657205..47667464,13	MCF-7	breast:
2	chr21:47574929..47577597-chr21:47652186..47654212,3	MCF-7	breast:
3	chr21:47653008..47655194-chr21:47704386..47706163,2	MCF-7	breast:
4	chr21:47649475..47654213-chr21:47668159..47671239,4	MCF-7	breast:
5	chr21:47651965..47653664-chr21:47792692..47794202,2	K562	blood:

No data

Variant related genes	Relation type
LSS	TF binding region
ENSG00000160282	Chromatin interaction
ENSG00000160294	Chromatin interaction
ENSG00000228137	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11089051	1.00[ASN][1000 genomes]
rs11908812	1.00[ASN][1000 genomes]
rs12482002	1.00[ASN][1000 genomes]
rs12482343	1.00[ASN][1000 genomes]
rs12482741	1.00[ASN][1000 genomes]
rs12482903	1.00[ASN][1000 genomes]
rs12482934	1.00[ASN][1000 genomes]
rs12483577	1.00[ASN][1000 genomes]
rs13046028	1.00[ASN][1000 genomes]
rs13047784	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979054	1.00[ASN][1000 genomes]
rs17176534	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17176737	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17176779	1.00[ASN][1000 genomes]
rs17176793	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17176800	1.00[ASN][1000 genomes]
rs17176905	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17176926	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17176974	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17176988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177030	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17182739	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17182746	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17183137	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17183151	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17183220	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17183368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17183417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17297798	1.00[ASN][1000 genomes]
rs17297961	1.00[ASN][1000 genomes]
rs17298556	1.00[ASN][1000 genomes]
rs17369792	1.00[ASN][1000 genomes]
rs2212749	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839169	1.00[ASN][1000 genomes]
rs34268261	1.00[ASN][1000 genomes]
rs34500739	1.00[ASN][1000 genomes]
rs56693387	1.00[ASN][1000 genomes]
rs59613587	1.00[ASN][1000 genomes]
rs60751239	1.00[ASN][1000 genomes]
rs61181882	1.00[ASN][1000 genomes]
rs61448213	1.00[ASN][1000 genomes]
rs61735811	1.00[ASN][1000 genomes]
rs61736728	1.00[ASN][1000 genomes]
rs62212860	1.00[ASN][1000 genomes]
rs62214040	1.00[ASN][1000 genomes]
rs62214041	1.00[ASN][1000 genomes]
rs62214042	1.00[ASN][1000 genomes]
rs62214043	1.00[ASN][1000 genomes]
rs62214045	1.00[ASN][1000 genomes]
rs62214046	1.00[ASN][1000 genomes]
rs62214051	1.00[ASN][1000 genomes]
rs62214052	1.00[ASN][1000 genomes]
rs62214055	1.00[ASN][1000 genomes]
rs62215182	1.00[ASN][1000 genomes]
rs62215183	1.00[ASN][1000 genomes]
rs62215184	1.00[ASN][1000 genomes]
rs62215186	1.00[ASN][1000 genomes]
rs62215187	1.00[ASN][1000 genomes]
rs8126678	1.00[ASN][1000 genomes]
rs8134519	1.00[ASN][1000 genomes]
rs9977340	1.00[ASN][1000 genomes]
rs9979331	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
14	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
15	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
16	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
17	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
18	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
19	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
20	nsv914134	chr21:47632995-47712185	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	n/a
21	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17183473	C21orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47649800-47654000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr21:47649800-47654200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr21:47649800-47654400	Weak transcription	Aorta	Aorta
4	chr21:47649800-47654400	Weak transcription	Colonic Mucosa	Colon
5	chr21:47649800-47654400	Weak transcription	Right Ventricle	heart
6	chr21:47649800-47701600	Weak transcription	Right Atrium	heart
7	chr21:47650000-47653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr21:47650000-47653800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr21:47650000-47654000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr21:47650000-47654000	Weak transcription	Brain Angular Gyrus	brain
11	chr21:47650000-47654000	Weak transcription	Brain Substantia Nigra	brain
12	chr21:47650000-47654000	Weak transcription	Colon Smooth Muscle	Colon
13	chr21:47650000-47654200	Weak transcription	Gastric	stomach
14	chr21:47650000-47654200	Weak transcription	Psoas Muscle	Psoas
15	chr21:47650000-47654200	Weak transcription	Spleen	Spleen
16	chr21:47650000-47654400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr21:47650000-47658600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr21:47650000-47658600	Weak transcription	Small Intestine	intestine
19	chr21:47650000-47705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr21:47650200-47653400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr21:47650200-47653600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr21:47650200-47653600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr21:47650200-47653600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr21:47650200-47653600	Weak transcription	Fetal Kidney	kidney
25	chr21:47650200-47653800	Weak transcription	Brain Anterior Caudate	brain
26	chr21:47650200-47653800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr21:47650200-47654000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr21:47650200-47654200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr21:47650200-47654800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr21:47650200-47667000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr21:47650400-47654000	Weak transcription	Fetal Brain Male	brain
32	chr21:47650400-47654400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr21:47650400-47654400	Weak transcription	Stomach Mucosa	stomach
34	chr21:47650400-47658800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr21:47650600-47653800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr21:47650600-47654000	Weak transcription	Fetal Heart	heart
37	chr21:47650600-47654600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr21:47650600-47656800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr21:47650600-47669800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr21:47650800-47654200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr21:47650800-47656600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr21:47650800-47701000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr21:47650800-47701400	Strong transcription	Fetal Muscle Leg	muscle
44	chr21:47650800-47701600	Strong transcription	Fetal Stomach	stomach
45	chr21:47651000-47653600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr21:47651000-47656800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr21:47651000-47656800	Strong transcription	NHEK	skin
48	chr21:47651000-47703200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr21:47651200-47653600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr21:47651200-47656800	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links