Variant report

Variant	rs12626961
Chromosome Location	chr21:47915275-47915276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47906465..47908075-chr21:47914315..47916689,2	MCF-7	breast:
2	chr21:47914976..47919873-chr21:47920315..47923447,4	K562	blood:
3	chr21:47877909..47879692-chr21:47914634..47916182,2	K562	blood:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1029262	0.96[ASN][1000 genomes]
rs11089066	0.84[ASN][1000 genomes]
rs11089068	0.90[ASN][1000 genomes]
rs11089069	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11089071	0.96[ASN][1000 genomes]
rs11089072	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089077	0.81[ASN][1000 genomes]
rs1123540	0.90[ASN][1000 genomes]
rs12185864	0.84[ASN][1000 genomes]
rs12482279	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12483081	0.95[ASN][1000 genomes]
rs12483421	0.90[ASN][1000 genomes]
rs12626200	0.90[ASN][1000 genomes]
rs12627331	0.92[ASN][1000 genomes]
rs12627653	0.96[ASN][1000 genomes]
rs13047052	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1977907	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012217	0.82[ASN][1000 genomes]
rs2032111	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2051190	0.87[ASN][1000 genomes]
rs2070426	0.87[ASN][1000 genomes]
rs2070434	0.94[ASN][1000 genomes]
rs2073374	0.87[ASN][1000 genomes]
rs2073376	0.86[ASN][1000 genomes]
rs2073377	0.87[ASN][1000 genomes]
rs2073381	0.90[ASN][1000 genomes]
rs2249970	0.90[ASN][1000 genomes]
rs2300563	0.86[ASN][1000 genomes]
rs2330594	0.96[ASN][1000 genomes]
rs2839257	0.86[ASN][1000 genomes]
rs2839261	0.86[ASN][1000 genomes]
rs2839265	0.90[ASN][1000 genomes]
rs2839268	0.90[ASN][1000 genomes]
rs2839270	0.85[ASN][1000 genomes]
rs2839275	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839276	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2839280	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839284	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839285	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839296	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2839297	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839299	0.94[ASN][1000 genomes]
rs2839313	0.97[ASN][1000 genomes]
rs2839317	0.95[ASN][1000 genomes]
rs34590323	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34736293	0.89[ASN][1000 genomes]
rs3747010	0.97[ASN][1000 genomes]
rs4267585	0.95[ASN][1000 genomes]
rs4431027	0.96[ASN][1000 genomes]
rs4819256	0.84[ASN][1000 genomes]
rs59500178	0.83[ASN][1000 genomes]
rs59977673	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62224256	0.81[ASN][1000 genomes]
rs62224257	0.90[ASN][1000 genomes]
rs62224258	0.90[ASN][1000 genomes]
rs62225682	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7279991	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8132022	0.90[ASN][1000 genomes]
rs9789884	0.95[ASN][1000 genomes]
rs9975345	0.85[ASN][1000 genomes]
rs9984247	0.84[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
15	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
16	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
18	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
19	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	30 gene(s)	inside rSNPs	n/a
20	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
21	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
22	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
23	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
24	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47880000-47916800	Weak transcription	Aorta	Aorta
2	chr21:47880200-47916600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:47880400-47916600	Weak transcription	Fetal Kidney	kidney
4	chr21:47880400-47916600	Weak transcription	HSMMtube	muscle
5	chr21:47880400-47918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:47880400-47918200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr21:47880400-47931200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr21:47889600-47918200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr21:47889800-47916800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:47892800-47920200	Weak transcription	Small Intestine	intestine
11	chr21:47899000-47918000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:47899200-47916800	Weak transcription	Colon Smooth Muscle	Colon
13	chr21:47900800-47917000	Weak transcription	Colonic Mucosa	Colon
14	chr21:47903400-47918400	Weak transcription	Brain Substantia Nigra	brain
15	chr21:47903600-47917000	Weak transcription	Brain Hippocampus Middle	brain
16	chr21:47903600-47918200	Weak transcription	Stomach Mucosa	stomach
17	chr21:47903600-47919200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr21:47904200-47918600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr21:47904200-47920200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr21:47904200-47920200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr21:47904200-47931200	Weak transcription	Psoas Muscle	Psoas
22	chr21:47904400-47918000	Weak transcription	Pancreas	Pancrea
23	chr21:47904600-47920200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr21:47904800-47918800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr21:47904800-47920200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr21:47905000-47920000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr21:47905000-47920600	Strong transcription	Placenta	Placenta
28	chr21:47905200-47919200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr21:47905400-47919200	Strong transcription	Primary T cells from cord blood	blood
30	chr21:47905400-47919200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr21:47905800-47920200	Strong transcription	Liver	Liver
32	chr21:47906200-47920400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr21:47906800-47918000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr21:47907000-47918000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr21:47907400-47919600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr21:47907800-47921000	Strong transcription	Dnd41	blood
37	chr21:47908000-47916600	Weak transcription	HepG2	liver
38	chr21:47908200-47916800	Weak transcription	NH-A	brain
39	chr21:47908600-47920200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr21:47908800-47919200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr21:47908800-47920200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr21:47909000-47919400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr21:47909000-47919800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr21:47909200-47920000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:47909200-47921000	Strong transcription	Fetal Intestine Large	intestine
46	chr21:47909400-47919000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr21:47909600-47916800	Weak transcription	Fetal Brain Male	brain
48	chr21:47909600-47932400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr21:47909800-47920000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr21:47910000-47916800	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links