Variant report

Variant	rs7959489
Chromosome Location	chr12:117592593-117592594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117584695..117586199-chr12:117591646..117594518,2	MCF-7	breast:
2	chr12:117589065..117590873-chr12:117591170..117593716,2	K562	blood:
3	chr12:117465400..117467600-chr12:117591439..117594342,2	MCF-7	breast:
4	chr12:117591837..117594892-chr12:117625944..117630228,6	K562	blood:
5	chr12:117587735..117590718-chr12:117591687..117594987,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135108	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10774905	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10850774	0.89[ASN][1000 genomes]
rs10850777	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10850782	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10850786	0.82[EUR][1000 genomes]
rs10850790	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs10850799	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs11068369	0.81[EUR][1000 genomes]
rs11068370	0.81[EUR][1000 genomes]
rs11068371	0.81[EUR][1000 genomes]
rs12304875	0.83[EUR][1000 genomes]
rs12310778	0.82[EUR][1000 genomes]
rs12322298	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12422378	0.82[EUR][1000 genomes]
rs1472522	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2036311	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2036312	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2062518	0.83[EUR][1000 genomes]
rs2062530	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2088699	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840100	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs3741472	0.81[EUR][1000 genomes]
rs4238053	0.83[EUR][1000 genomes]
rs4492907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766831	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766834	0.83[EUR][1000 genomes]
rs4767502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767503	0.82[EUR][1000 genomes]
rs4767504	0.82[EUR][1000 genomes]
rs4767505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767506	0.82[EUR][1000 genomes]
rs4767507	0.82[EUR][1000 genomes]
rs4767511	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs4767512	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767514	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767515	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767518	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4767519	0.84[EUR][1000 genomes]
rs6490117	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67383912	0.88[EUR][1000 genomes]
rs7297713	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307866	0.82[ASN][1000 genomes]
rs7313745	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953808	0.91[ASN][1000 genomes]
rs7957758	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884282	0.89[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv899542	chr12:117549739-117623136	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active 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	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7959489	FBXO21	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117572400-117596000	Weak transcription	Fetal Brain Male	brain
2	chr12:117578200-117617200	Strong transcription	Fetal Stomach	stomach
3	chr12:117579000-117618200	Strong transcription	Thymus	Thymus
4	chr12:117579200-117602600	Weak transcription	Psoas Muscle	Psoas
5	chr12:117579200-117623000	Strong transcription	Primary T cells from cord blood	blood
6	chr12:117579400-117616800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:117580000-117593400	Weak transcription	Small Intestine	intestine
8	chr12:117580000-117625000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr12:117580000-117626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:117580400-117593600	Weak transcription	HSMM	muscle
11	chr12:117580400-117618800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:117580600-117625600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:117581200-117618400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:117581200-117624600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:117581400-117624200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:117581400-117625800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:117581600-117593000	Strong transcription	Fetal Intestine Large	intestine
18	chr12:117581600-117618800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:117582000-117593200	Strong transcription	Fetal Intestine Small	intestine
20	chr12:117582000-117613200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:117582200-117606200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:117582200-117623400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr12:117582200-117625800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:117582400-117594000	Strong transcription	Gastric	stomach
25	chr12:117582400-117624400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:117582600-117608400	Strong transcription	Liver	Liver
27	chr12:117584000-117595400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:117585600-117619000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr12:117585600-117619800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:117585800-117600600	Strong transcription	Primary B cells from cord blood	blood
31	chr12:117585800-117602800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:117585800-117625600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:117586800-117596000	Strong transcription	Hela-S3	cervix
34	chr12:117587000-117592600	Weak transcription	NHDF-Ad	bronchial
35	chr12:117587000-117593400	Strong transcription	Esophagus	oesophagus
36	chr12:117588600-117592600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:117588600-117592800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:117588800-117618800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:117588800-117619000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:117589200-117593200	Strong transcription	Spleen	Spleen
41	chr12:117589400-117604000	Weak transcription	Fetal Heart	heart
42	chr12:117589400-117623600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:117589600-117614600	Strong transcription	Lung	lung
44	chr12:117589600-117619400	Strong transcription	Brain Germinal Matrix	brain
45	chr12:117589800-117601000	Strong transcription	Brain Angular Gyrus	brain
46	chr12:117589800-117618800	Strong transcription	Fetal Brain Female	brain
47	chr12:117590000-117593400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:117590000-117595600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:117590000-117596000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:117590000-117599000	Weak transcription	Stomach Mucosa	stomach

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