Variant report

Variant	rs3788180
Chromosome Location	chr21:46625120-46625121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46618280..46621983-chr21:46623328..46625308,3	K562	blood:
2	chr21:46624737..46628208-chr21:46629925..46633186,4	K562	blood:
3	chr21:46622478..46626283-chr21:46626862..46631203,5	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11088982	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12185823	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13047803	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537121	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1556317	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2150439	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838797	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838803	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838807	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28782181	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs372766	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs377524	0.84[ASN][1000 genomes]
rs384876	0.84[ASN][1000 genomes]
rs386762	0.84[ASN][1000 genomes]
rs422720	0.84[ASN][1000 genomes]
rs434492	0.84[ASN][1000 genomes]
rs446158	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4819030	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4819031	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6518214	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7281416	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7281757	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8126717	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8126895	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128889	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130224	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8133307	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8134789	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs983749	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9974232	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv587841	chr21:46619840-46647078	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3788180	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46589000-46646000	Weak transcription	Colonic Mucosa	Colon
2	chr21:46606000-46630600	Weak transcription	Pancreas	Pancrea
3	chr21:46606800-46628400	Weak transcription	NH-A	brain
4	chr21:46606800-46640800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr21:46607600-46628600	Weak transcription	Osteobl	bone
6	chr21:46609000-46630600	Weak transcription	Fetal Thymus	thymus
7	chr21:46609000-46630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:46609600-46634600	Weak transcription	Fetal Heart	heart
9	chr21:46610000-46634800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr21:46610000-46644800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr21:46610200-46634400	Weak transcription	Psoas Muscle	Psoas
12	chr21:46610400-46641000	Weak transcription	Brain Germinal Matrix	brain
13	chr21:46610400-46641800	Weak transcription	HepG2	liver
14	chr21:46610800-46640200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr21:46610800-46641000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr21:46610800-46641200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr21:46610800-46647800	Weak transcription	Brain Angular Gyrus	brain
18	chr21:46611000-46625200	Weak transcription	Liver	Liver
19	chr21:46611000-46639600	Weak transcription	Fetal Brain Male	brain
20	chr21:46611000-46639600	Weak transcription	Gastric	stomach
21	chr21:46611000-46644600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr21:46611000-46645000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr21:46611200-46629200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr21:46611200-46630800	Weak transcription	Fetal Intestine Large	intestine
25	chr21:46613000-46628000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr21:46616600-46627200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr21:46617600-46632600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr21:46618800-46625800	Strong transcription	Aorta	Aorta
29	chr21:46619000-46625800	Strong transcription	Fetal Stomach	stomach
30	chr21:46619000-46633000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr21:46619200-46625600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr21:46619600-46625800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:46619600-46627000	Weak transcription	HMEC	breast
34	chr21:46620600-46628000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr21:46620800-46627800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr21:46620800-46633600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr21:46621000-46626200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr21:46621000-46627000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr21:46621000-46629200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr21:46621200-46628000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr21:46621200-46628000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr21:46621200-46633400	Strong transcription	HSMMtube	muscle
43	chr21:46621400-46627800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr21:46621800-46625600	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr21:46621800-46640400	Weak transcription	Fetal Brain Female	brain
46	chr21:46622000-46640600	Weak transcription	Brain Substantia Nigra	brain
47	chr21:46622200-46625400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr21:46622200-46627200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr21:46622200-46628200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr21:46622200-46632600	Strong transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links