Variant report

Variant	rs13053002
Chromosome Location	chr21:46677854-46677855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46675525..46679390-chr21:46682642..46685767,4	MCF-7	breast:
2	chr21:46677076..46679332-chr21:46681439..46683653,2	MCF-7	breast:
3	chr21:46493414..46496701-chr21:46675649..46680419,4	K562	blood:
4	chr21:46671702..46674861-chr21:46675485..46679113,5	K562	blood:
5	chr21:46677419..46679156-chr21:46838210..46839952,2	MCF-7	breast:
6	chr21:46672166..46673879-chr21:46677164..46679113,2	K562	blood:
7	chr21:46677096..46679104-chr21:46679185..46682740,7	K562	blood:
8	chr21:46675057..46677884-chr21:47243864..47245535,2	MCF-7	breast:
9	chr21:46676803..46681179-chr21:46705386..46709769,5	MCF-7	breast:
10	chr21:46675852..46678920-chr21:46700237..46703123,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000186866	Chromatin interaction
ENSG00000215447	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11910831	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13047688	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13049700	0.83[ASN][1000 genomes]
rs13052356	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2236444	0.80[EUR][1000 genomes]
rs2236449	0.85[ASN][1000 genomes]
rs2297283	0.88[ASN][1000 genomes]
rs2297284	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297285	0.89[EUR][1000 genomes]
rs2297286	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2330013	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2838830	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2838847	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28628220	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34211339	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34886433	0.96[EUR][1000 genomes]
rs3746980	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818769	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4819052	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs733738	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs733739	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8130866	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs914217	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9306123	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9976074	0.88[EUR][1000 genomes]
rs9984901	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv1059779	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	nsv544485	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv1059805	chr21:46618210-46736943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv913999	chr21:46636844-46765251	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv914000	chr21:46647078-46765251	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
19	nsv914001	chr21:46647078-46944113	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
20	nsv914002	chr21:46655638-46945024	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
21	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
22	nsv914003	chr21:46670874-46695039	Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv914004	chr21:46670874-46736694	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
24	nsv914005	chr21:46670874-46756700	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
25	nsv914006	chr21:46670874-46788299	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13053002	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46669000-46683400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr21:46669200-46706600	Weak transcription	Right Atrium	heart
3	chr21:46671200-46683000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr21:46673400-46681600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr21:46673800-46683400	Weak transcription	HSMM	muscle
6	chr21:46674400-46678200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:46674600-46678000	Enhancers	Fetal Thymus	thymus
8	chr21:46674600-46678400	Enhancers	Primary hematopoietic stem cells	blood
9	chr21:46675000-46678000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr21:46675200-46678600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr21:46675600-46682400	Weak transcription	Pancreas	Pancrea
12	chr21:46675600-46686200	Weak transcription	GM12878-XiMat	blood
13	chr21:46675800-46679000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr21:46676000-46678400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:46676000-46706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr21:46676200-46678000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr21:46676200-46678200	Bivalent Enhancer	Placenta	Placenta
18	chr21:46676200-46678600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr21:46676400-46678000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr21:46676400-46678000	Enhancers	Fetal Heart	heart
21	chr21:46676400-46678600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr21:46676600-46678200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:46676600-46678200	Bivalent Enhancer	Fetal Stomach	stomach
24	chr21:46676800-46681800	Weak transcription	Spleen	Spleen
25	chr21:46677000-46678000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
26	chr21:46677000-46678600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr21:46677000-46682600	Weak transcription	Thymus	Thymus
28	chr21:46677000-46683400	Weak transcription	Primary T cells from cord blood	blood
29	chr21:46677000-46683800	Weak transcription	Primary B cells from cord blood	blood
30	chr21:46677200-46678000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr21:46677200-46678400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr21:46677200-46681600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr21:46677200-46682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr21:46677200-46682600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr21:46677200-46683200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr21:46677200-46683200	Weak transcription	Left Ventricle	heart
37	chr21:46677400-46678000	Bivalent Enhancer	Colonic Mucosa	Colon
38	chr21:46677400-46678800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr21:46677400-46678800	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr21:46677400-46679000	Bivalent Enhancer	HepG2	liver
41	chr21:46677400-46681800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr21:46677400-46683200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr21:46677400-46683200	Weak transcription	Right Ventricle	heart
44	chr21:46677400-46683600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr21:46677400-46683600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr21:46677600-46678600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr21:46677600-46679000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr21:46677600-46680400	Weak transcription	HSMMtube	muscle
49	chr21:46677600-46681400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr21:46677600-46683200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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