Variant report

Variant	rs7279959
Chromosome Location	chr21:45107518-45107519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45082895..45085626-chr21:45107142..45109564,2	MCF-7	breast:
2	chr21:45105070..45107899-chr21:45137956..45140399,2	MCF-7	breast:
3	chr21:45101692..45105011-chr21:45106889..45110071,3	MCF-7	breast:
4	chr21:45102484..45105082-chr21:45106638..45109482,2	K562	blood:

Variant related genes	Relation type
ENSG00000160209	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1003280	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1073522	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1122873	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs11700909	0.93[JPT][hapmap]
rs11702544	0.90[ASN][1000 genomes]
rs11909064	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12627667	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1378079	0.86[CHB][hapmap]
rs1378080	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs141521	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1454648	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1454650	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1454651	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1584917	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1584918	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1598206	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs162344	0.86[CHB][hapmap]
rs162345	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs162366	0.86[CHB][hapmap]
rs162371	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs162372	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs162375	0.86[CHB][hapmap]
rs162376	0.86[CHB][hapmap]
rs162377	0.86[CHB][hapmap]
rs162378	0.86[CHB][hapmap]
rs162388	0.86[CHB][hapmap]
rs2070533	0.93[JPT][hapmap]
rs2155722	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2186924	0.86[JPT][hapmap]
rs2236665	0.93[ASN][1000 genomes]
rs2236666	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2236667	0.93[ASN][1000 genomes]
rs2246602	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2250773	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2251253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2282526	0.88[ASN][1000 genomes]
rs229357	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2298561	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2298562	0.90[ASN][1000 genomes]
rs2329442	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2329593	0.93[JPT][hapmap]
rs2838316	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838317	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838319	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838320	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2838321	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838323	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838324	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838328	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838330	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838331	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838336	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2838337	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838338	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2838339	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2838341	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2838343	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2838344	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2838345	0.93[ASN][1000 genomes]
rs2838348	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2838350	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2838351	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2838353	0.93[JPT][hapmap]
rs2838354	0.93[JPT][hapmap]
rs3788062	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs3819161	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs389278	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4818850	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4818858	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4818859	0.93[JPT][hapmap]
rs4818860	0.93[JPT][hapmap]
rs4819270	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4819283	0.90[ASN][1000 genomes]
rs4819285	0.93[JPT][hapmap]
rs4819288	0.93[JPT][hapmap]
rs4819289	0.93[JPT][hapmap]
rs4819291	0.92[JPT][hapmap]
rs4819295	0.93[JPT][hapmap]
rs4819296	0.93[JPT][hapmap]
rs6518301	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs6518302	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs6518309	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6518310	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7276215	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7276633	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7277539	0.87[JPT][hapmap]
rs7279958	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7279968	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7282122	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs762400	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8129601	0.93[JPT][hapmap]
rs8133523	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs86139	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9306159	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9306160	0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs969060	0.87[ASN][1000 genomes]
rs9941787	0.88[ASN][1000 genomes]
rs9976441	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs9977076	0.90[ASN][1000 genomes]
rs9978811	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs9978858	0.90[ASN][1000 genomes]
rs9980185	0.87[JPT][hapmap]
rs9981072	1.00[CEU][hapmap]
rs9981291	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs9981790	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs9982727	0.90[ASN][1000 genomes]
rs9983670	0.90[ASN][1000 genomes]
rs9983763	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs9984002	0.87[JPT][hapmap]

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	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
4	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
5	nsv1066728	chr21:45089877-45131723	Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45080600-45122400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45080800-45121800	Weak transcription	Fetal Heart	heart
3	chr21:45080800-45122600	Weak transcription	Small Intestine	intestine
4	chr21:45082800-45116600	Strong transcription	Primary T cells from cord blood	blood
5	chr21:45086000-45117200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:45086400-45110600	Weak transcription	Stomach Mucosa	stomach
7	chr21:45088400-45117200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr21:45088600-45116400	Strong transcription	Dnd41	blood
9	chr21:45088600-45117000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr21:45088800-45118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:45089000-45117000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr21:45089000-45117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr21:45089000-45117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr21:45089200-45115000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:45089200-45116000	Strong transcription	Fetal Thymus	thymus
16	chr21:45089200-45116200	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr21:45089200-45117000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr21:45089200-45117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr21:45089400-45116600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr21:45089600-45116400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr21:45089600-45116400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr21:45089800-45107800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr21:45089800-45108000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr21:45089800-45117000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr21:45089800-45117200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr21:45090000-45107800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr21:45093800-45112200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr21:45093800-45117000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr21:45094000-45117600	Strong transcription	Fetal Intestine Small	intestine
30	chr21:45094200-45116200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr21:45094600-45114600	Strong transcription	Brain Substantia Nigra	brain
32	chr21:45094600-45116200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr21:45094600-45116600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr21:45094600-45117200	Strong transcription	Fetal Stomach	stomach
35	chr21:45094800-45107800	Strong transcription	Thymus	Thymus
36	chr21:45094800-45116400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr21:45094800-45117200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr21:45094800-45122000	Weak transcription	Right Atrium	heart
39	chr21:45095000-45115000	Strong transcription	Fetal Brain Female	brain
40	chr21:45095200-45116400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr21:45095400-45117000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr21:45097400-45108000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr21:45097600-45109800	Weak transcription	Fetal Brain Male	brain
44	chr21:45099200-45116200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr21:45099600-45109200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr21:45099600-45115400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr21:45100000-45114800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr21:45100000-45116400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr21:45100000-45116800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr21:45100000-45117200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links