Variant report

Variant	rs9978858
Chromosome Location	chr21:45085552-45085553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45084057..45085743-chr21:45138853..45140795,2	MCF-7	breast:
2	chr21:44775127..44777356-chr21:45085128..45087430,2	MCF-7	breast:
3	chr21:45083913..45086449-chr21:45100851..45103835,2	MCF-7	breast:
4	chr21:45082895..45085626-chr21:45107142..45109564,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160209	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10211901	0.82[EUR][1000 genomes]
rs11089093	0.85[EUR][1000 genomes]
rs11700909	0.87[EUR][1000 genomes]
rs11700913	0.92[EUR][1000 genomes]
rs11702544	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11909064	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051953	0.91[EUR][1000 genomes]
rs2006113	0.91[EUR][1000 genomes]
rs2051407	0.84[EUR][1000 genomes]
rs2070533	0.92[EUR][1000 genomes]
rs2155722	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236665	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236666	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236667	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250773	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251253	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282526	0.95[ASN][1000 genomes]
rs2298562	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329443	0.88[AFR][1000 genomes]
rs2329593	0.92[EUR][1000 genomes]
rs2838344	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838345	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838348	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838350	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838351	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838353	0.80[ASN][1000 genomes]
rs2838354	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3819161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818858	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818859	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4818860	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4818861	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4819283	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819285	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819286	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819287	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819288	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4819289	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4819290	0.84[EUR][1000 genomes]
rs4819291	0.92[EUR][1000 genomes]
rs4819292	0.91[EUR][1000 genomes]
rs4819293	0.91[EUR][1000 genomes]
rs4819294	0.91[EUR][1000 genomes]
rs6518309	0.94[AFR][1000 genomes]
rs6518310	0.96[ASN][1000 genomes]
rs7277539	0.80[EUR][1000 genomes]
rs7279959	0.90[ASN][1000 genomes]
rs7282122	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282405	0.92[EUR][1000 genomes]
rs7283428	0.90[EUR][1000 genomes]
rs762400	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8129601	0.80[ASN][1000 genomes]
rs8131111	0.90[EUR][1000 genomes]
rs8133276	0.91[EUR][1000 genomes]
rs914197	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs914198	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9306160	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs969060	0.94[ASN][1000 genomes]
rs9941787	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9977076	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9982727	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9983670	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

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	chr21:45080800-45085600	Weak transcription	Right Ventricle	heart
4	chr21:45080800-45085600	Weak transcription	Stomach Mucosa	stomach
5	chr21:45080800-45087000	Weak transcription	Osteobl	bone
6	chr21:45080800-45089200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:45080800-45089400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr21:45080800-45092000	Weak transcription	Esophagus	oesophagus
9	chr21:45080800-45094600	Weak transcription	NHLF	lung
10	chr21:45080800-45094800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr21:45080800-45094800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr21:45080800-45096200	Weak transcription	Psoas Muscle	Psoas
13	chr21:45080800-45121800	Weak transcription	Fetal Heart	heart
14	chr21:45080800-45122600	Weak transcription	Small Intestine	intestine
15	chr21:45081000-45089800	Weak transcription	NH-A	brain
16	chr21:45081200-45085600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:45081200-45085800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr21:45081200-45085800	Weak transcription	Colon Smooth Muscle	Colon
19	chr21:45081200-45089200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr21:45081200-45096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr21:45081400-45085600	Weak transcription	Liver	Liver
22	chr21:45081400-45085600	Weak transcription	Fetal Lung	lung
23	chr21:45081400-45085600	Strong transcription	Fetal Stomach	stomach
24	chr21:45081400-45086000	Strong transcription	Fetal Muscle Leg	muscle
25	chr21:45081400-45086200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr21:45081400-45086200	Strong transcription	Fetal Intestine Small	intestine
27	chr21:45081400-45089800	Weak transcription	NHDF-Ad	bronchial
28	chr21:45081600-45085800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr21:45081600-45086400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr21:45081600-45086400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:45081600-45086400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr21:45081600-45086400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr21:45081600-45086400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr21:45081600-45086400	Strong transcription	Fetal Intestine Large	intestine
35	chr21:45081600-45086400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr21:45081600-45086600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr21:45081600-45087200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr21:45081600-45087600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr21:45081600-45093800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr21:45081800-45085800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr21:45081800-45086400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr21:45081800-45086400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr21:45081800-45087200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr21:45081800-45087400	Strong transcription	Fetal Thymus	thymus
45	chr21:45081800-45087600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr21:45082000-45086400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr21:45082000-45086400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr21:45082000-45101800	Weak transcription	Fetal Kidney	kidney
49	chr21:45082000-45107200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr21:45082200-45085600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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