Variant report

Variant	rs28405975
Chromosome Location	chr21:45087876-45087877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45085920..45088210-chr21:45131139..45133231,2	MCF-7	breast:
2	chr21:45087874..45089696-chr21:45094798..45096349,2	MCF-7	breast:
3	chr21:45087767..45089623-chr21:45137418..45140191,2	K562	blood:

Variant related genes	Relation type
ENSG00000160209	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1041455	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11911865	1.00[EUR][1000 genomes]
rs12165286	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2329600	1.00[EUR][1000 genomes]
rs4383428	0.89[AFR][1000 genomes]
rs61737067	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs718470	1.00[EUR][1000 genomes]
rs73369437	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73908376	1.00[EUR][1000 genomes]
rs8133686	0.81[AFR][1000 genomes]
rs9974513	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9977102	0.81[AFR][1000 genomes]
rs9977212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9978403	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9978934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9979935	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9980578	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9983752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9984720	0.83[AFR][1000 genomes]
rs9984724	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834106	chr21:44992387-45109489	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv587700	chr21:45007956-45095200	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv913874	chr21:45041790-45191005	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active 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	36 gene(s)	inside rSNPs	diseases
5	nsv531544	chr21:45071371-45202912	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv999311	chr21:45087738-45097588	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45080200-45089800	Weak transcription	Aorta	Aorta
2	chr21:45080600-45122400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:45080800-45089200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:45080800-45089400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr21:45080800-45092000	Weak transcription	Esophagus	oesophagus
6	chr21:45080800-45094600	Weak transcription	NHLF	lung
7	chr21:45080800-45094800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr21:45080800-45094800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:45080800-45096200	Weak transcription	Psoas Muscle	Psoas
10	chr21:45080800-45121800	Weak transcription	Fetal Heart	heart
11	chr21:45080800-45122600	Weak transcription	Small Intestine	intestine
12	chr21:45081000-45089800	Weak transcription	NH-A	brain
13	chr21:45081200-45089200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr21:45081200-45096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr21:45081400-45089800	Weak transcription	NHDF-Ad	bronchial
16	chr21:45081600-45093800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:45082000-45101800	Weak transcription	Fetal Kidney	kidney
18	chr21:45082000-45107200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr21:45082400-45089200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr21:45082400-45089800	Weak transcription	Left Ventricle	heart
21	chr21:45082400-45097200	Weak transcription	Fetal Brain Male	brain
22	chr21:45082600-45089400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr21:45082800-45089800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr21:45082800-45096200	Weak transcription	Colonic Mucosa	Colon
25	chr21:45082800-45116600	Strong transcription	Primary T cells from cord blood	blood
26	chr21:45083400-45089800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr21:45083400-45089800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr21:45084600-45090400	Weak transcription	HSMM	muscle
29	chr21:45085000-45089800	Weak transcription	Brain Anterior Caudate	brain
30	chr21:45085000-45089800	Weak transcription	Brain Substantia Nigra	brain
31	chr21:45085000-45090200	Weak transcription	HSMMtube	muscle
32	chr21:45085200-45089800	Weak transcription	Brain Angular Gyrus	brain
33	chr21:45085200-45089800	Weak transcription	Brain Hippocampus Middle	brain
34	chr21:45085200-45089800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr21:45085200-45094600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr21:45085400-45089800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr21:45085400-45090400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr21:45085800-45089800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr21:45085800-45095000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr21:45086000-45089800	Weak transcription	Liver	Liver
41	chr21:45086000-45089800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr21:45086000-45117200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr21:45086200-45088600	Weak transcription	Dnd41	blood
44	chr21:45086200-45088600	Weak transcription	K562	blood
45	chr21:45086200-45089200	Weak transcription	Fetal Brain Female	brain
46	chr21:45086200-45089400	Weak transcription	Ovary	ovary
47	chr21:45086200-45089800	Weak transcription	Right Ventricle	heart
48	chr21:45086200-45089800	Weak transcription	Hela-S3	cervix
49	chr21:45086200-45090000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr21:45086200-45094000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links