Variant report

Variant	rs28782181
Chromosome Location	chr21:46588817-46588818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr21:46588410-46589209	PBDE	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46586605..46588915-chr21:46675140..46677229,2	K562	blood:
2	chr21:46586995..46592553-chr21:46595453..46599761,7	K562	blood:
3	chr21:46574123..46577749-chr21:46583837..46588993,5	K562	blood:
4	chr21:46582653..46585265-chr21:46586911..46589357,3	MCF-7	breast:
5	chr21:46588242..46590449-chr21:46597999..46599761,2	K562	blood:
6	chr21:46587207..46589418-chr21:46711709..46714315,2	K562	blood:

No data

Variant related genes	Relation type
ADARB1	TF binding region
ENSG00000223768	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11088982	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12185823	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13047803	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1537121	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1556317	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2150439	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2838797	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838803	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838807	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs365791	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs372766	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374778	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs377524	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3788180	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs381466	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs384876	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs386762	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs422720	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434492	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs446158	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4819030	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4819031	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6518214	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7281416	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7281757	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8126717	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8126895	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8128889	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8130224	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8133307	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8134789	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs983749	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9974232	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	esv1802303	chr21:46580319-46606676	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28782181	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr21:46557200-46591800	Weak transcription	HUVEC	blood vessel
3	chr21:46563000-46595600	Weak transcription	Pancreas	Pancrea
4	chr21:46572200-46595600	Weak transcription	Brain Germinal Matrix	brain
5	chr21:46572400-46601000	Weak transcription	Fetal Brain Female	brain
6	chr21:46572800-46604800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr21:46573600-46591800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr21:46574200-46589200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr21:46575000-46595600	Weak transcription	Dnd41	blood
10	chr21:46575000-46601000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr21:46575400-46589000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr21:46575400-46604800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr21:46576200-46595800	Weak transcription	Fetal Lung	lung
14	chr21:46580400-46591800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr21:46580400-46595600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr21:46582000-46590200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr21:46582400-46589000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:46582400-46589400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr21:46582400-46595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr21:46582400-46595600	Weak transcription	Gastric	stomach
21	chr21:46582600-46591000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:46582600-46598000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr21:46582800-46592000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr21:46583400-46589000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr21:46583400-46589000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr21:46583400-46589000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr21:46583400-46589800	Enhancers	Colon Smooth Muscle	Colon
28	chr21:46583600-46591000	Weak transcription	Primary B cells from cord blood	blood
29	chr21:46583800-46589000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr21:46583800-46589000	Weak transcription	Esophagus	oesophagus
31	chr21:46583800-46592000	Weak transcription	Fetal Stomach	stomach
32	chr21:46583800-46596200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr21:46583800-46606000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr21:46584000-46596600	Weak transcription	Brain Angular Gyrus	brain
35	chr21:46584400-46595600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr21:46584800-46589000	Weak transcription	Brain Anterior Caudate	brain
37	chr21:46584800-46590000	Enhancers	HSMMtube	muscle
38	chr21:46584800-46591800	Weak transcription	Spleen	Spleen
39	chr21:46585000-46592000	Weak transcription	Right Ventricle	heart
40	chr21:46585000-46592400	Weak transcription	Lung	lung
41	chr21:46585200-46589000	Weak transcription	Fetal Muscle Leg	muscle
42	chr21:46586400-46589800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr21:46586400-46591600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr21:46587000-46589000	Enhancers	Stomach Smooth Muscle	stomach
45	chr21:46587200-46589600	Enhancers	Osteobl	bone
46	chr21:46587200-46589800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr21:46587200-46596000	Weak transcription	Ovary	ovary
48	chr21:46587200-46600200	Weak transcription	Liver	Liver
49	chr21:46587600-46589000	Weak transcription	Aorta	Aorta
50	chr21:46587600-46590000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links