Variant report

Variant	rs5029459
Chromosome Location	chr11:10480466-10480467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr11:10480387-10481059	GM12878	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
2	RUNX3	chr11:10480297-10481342	GM12878	blood:	n/a	n/a
3	SPI1	chr11:10480399-10481399	HL-60	blood:	n/a	chr11:10480649-10480662
4	RELA	chr11:10480346-10481100	GM18951	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
5	RCOR1	chr11:10480440-10480993	K562	blood:	n/a	n/a
6	POLR2A	chr11:10480360-10481203	GM12892	blood:	n/a	n/a
7	SPI1	chr11:10480446-10480955	GM12878	blood:	n/a	chr11:10480649-10480662
8	ELF1	chr11:10480379-10481059	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:10480463-10481206	GM12892	blood:	n/a	n/a
10	RELA	chr11:10480414-10481279	GM12892	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
11	EBF1	chr11:10480440-10481143	GM12878	blood:	n/a	n/a
12	ATF2	chr11:10480383-10481062	GM12878	blood:	n/a	n/a
13	RELA	chr11:10480428-10481364	GM15510	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
14	BCLAF1	chr11:10480449-10480918	GM12878	blood:	n/a	n/a
15	IRF1	chr11:10480380-10480698	K562	blood:	n/a	chr11:10480502-10480522 chr11:10480508-10480519 chr11:10480507-10480521 chr11:10480508-10480521 chr11:10480507-10480521
16	PAX5	chr11:10480325-10481098	GM12878	blood:	n/a	n/a
17	WRNIP1	chr11:10480413-10481402	GM12878	blood:	n/a	n/a
18	NFIC	chr11:10480334-10481155	GM12878	blood:	n/a	n/a
19	BCLAF1	chr11:10480390-10481130	GM12878	blood:	n/a	n/a
20	REST	chr11:10480383-10481558	HL-60	blood:	n/a	chr11:10481083-10481092
21	RELA	chr11:10480381-10481323	GM19099	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
22	YY1	chr11:10480373-10481206	GM12892	blood:	n/a	n/a
23	SPI1	chr11:10480400-10481159	GM12878	blood:	n/a	chr11:10480649-10480662
24	SPI1	chr11:10480430-10481197	GM12891	blood:	n/a	chr11:10480649-10480662
25	POLR2A	chr11:10480436-10481187	GM12892	blood:	n/a	n/a
26	MAZ	chr11:10480459-10481241	GM12878	blood:	n/a	n/a
27	CHD2	chr11:10480334-10481150	GM12878	blood:	n/a	chr11:10480491-10480501
28	RELA	chr11:10480350-10481357	GM12891	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
29	POLR2A	chr11:10480435-10481104	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:10480332-10481301	GM12892	blood:	n/a	n/a
31	RUNX3	chr11:10480380-10481324	GM12878	blood:	n/a	n/a
32	ATF2	chr11:10480393-10481021	GM12878	blood:	n/a	n/a
33	EP300	chr11:10480375-10480962	GM12878	blood:	n/a	chr11:10480759-10480772 chr11:10480852-10480859 chr11:10480652-10480666 chr11:10480646-10480660
34	RELA	chr11:10480374-10481197	GM19193	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
35	RELA	chr11:10480270-10481178	GM18505	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
36	YY1	chr11:10480420-10480877	GM12878	blood:	n/a	n/a
37	PML	chr11:10480358-10481124	GM12878	blood:	n/a	n/a
38	RELA	chr11:10480413-10481399	GM10847	blood:	n/a	chr11:10480629-10480638 chr11:10480629-10480638
39	SPI1	chr11:10480422-10480884	GM12891	blood:	n/a	chr11:10480649-10480662
40	YY1	chr11:10480424-10480885	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10470733..10474944-chr11:10476648..10480616,5	MCF-7	breast:

Variant related genes	Relation type
AMPD3	TF binding region
ENSG00000133805	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11042826	0.83[AMR][1000 genomes]
rs2403330	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58115104	0.80[AFR][1000 genomes]
rs58910510	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61314883	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73407718	0.80[AMR][1000 genomes]
rs73407783	0.84[EUR][1000 genomes]
rs73409935	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73409946	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs922359	0.85[AFR][1000 genomes];0.86[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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv896990	chr11:10458596-10514707	Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10473200-10512000	Weak transcription	Aorta	Aorta
2	chr11:10474200-10482800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:10476400-10481400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr11:10476600-10481400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:10476800-10482600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr11:10477000-10481000	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr11:10477000-10481400	Flanking Active TSS	Dnd41	blood
8	chr11:10477000-10481600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr11:10477200-10480600	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr11:10477200-10481400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr11:10477200-10481400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:10477800-10489000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:10478000-10480600	Weak transcription	Left Ventricle	heart
14	chr11:10478000-10487400	Weak transcription	HMEC	breast
15	chr11:10478200-10480600	Weak transcription	Fetal Heart	heart
16	chr11:10478200-10481200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr11:10478200-10482600	Weak transcription	Stomach Mucosa	stomach
18	chr11:10478200-10482600	Weak transcription	HSMMtube	muscle
19	chr11:10478200-10483200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:10478200-10485800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:10478400-10480600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:10478400-10480600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:10478400-10480600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:10478400-10480800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:10478400-10480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:10478400-10481000	Weak transcription	Small Intestine	intestine
27	chr11:10478400-10482600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:10478400-10483800	Weak transcription	Gastric	stomach
29	chr11:10478400-10484600	Weak transcription	Liver	Liver
30	chr11:10478400-10484800	Weak transcription	Osteobl	bone
31	chr11:10478400-10486000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:10478400-10487200	Weak transcription	Fetal Intestine Large	intestine
33	chr11:10478400-10487400	Weak transcription	Right Ventricle	heart
34	chr11:10478400-10489000	Weak transcription	A549	lung
35	chr11:10478400-10500000	Weak transcription	Fetal Intestine Small	intestine
36	chr11:10478400-10502800	Weak transcription	Pancreas	Pancrea
37	chr11:10478600-10480800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr11:10478600-10481000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:10478600-10481600	Enhancers	Brain Cingulate Gyrus	brain
40	chr11:10478600-10483400	Weak transcription	Colonic Mucosa	Colon
41	chr11:10478800-10480600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr11:10478800-10480800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr11:10478800-10482800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:10478800-10483000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:10478800-10493600	Weak transcription	HSMM	muscle
46	chr11:10478800-10511600	Weak transcription	Psoas Muscle	Psoas
47	chr11:10479000-10480600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr11:10479000-10480600	Weak transcription	Adipose Nuclei	Adipose
49	chr11:10479000-10480600	Weak transcription	Fetal Muscle Leg	muscle
50	chr11:10479000-10481200	Enhancers	Lung	lung

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