Variant report

Variant	rs58528246
Chromosome Location	chr11:47269369-47269370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:47268991-47271448	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr11:47269274-47271302	SK-N-SH	brain:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47197588..47201043-chr11:47267472..47270431,4	MCF-7	breast:
2	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
3	chr11:47234882..47238296-chr11:47268822..47272499,5	MCF-7	breast:
4	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:
5	chr11:47268303..47273264-chr11:47289525..47294481,12	K562	blood:
6	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
7	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
8	chr11:47201377..47203716-chr11:47267132..47269463,2	K562	blood:
9	chr11:47267881..47272421-chr11:47288787..47294481,12	K562	blood:
10	chr11:47197356..47201056-chr11:47268366..47272336,6	MCF-7	breast:
11	chr11:47263774..47268457-chr11:47268937..47272422,6	MCF-7	breast:
12	chr11:47235800..47238158-chr11:47268993..47270943,3	MCF-7	breast:
13	chr11:47269329..47270011-chr5:138533529..138534197,2	Hela-S3	cervix:
14	chr11:47205635..47209843-chr11:47268961..47271979,7	MCF-7	breast:
15	chr11:47268938..47272778-chr11:47288986..47293565,7	MCF-7	breast:

No data

Variant related genes	Relation type
NR1H3	TF binding region
ACP2	TF binding region
ENSG00000110514	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000120725	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1050244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039160	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11039161	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11039177	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11039179	1.00[AMR][1000 genomes]
rs11039185	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11530167	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3729936	1.00[AMR][1000 genomes]
rs3729948	0.90[EUR][1000 genomes]
rs3729953	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3729991	1.00[AMR][1000 genomes]
rs45603841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647718	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647730	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647731	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647738	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647752	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56023479	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57741802	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57852039	0.93[EUR][1000 genomes]
rs58912703	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61124822	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110333	1.00[AMR][1000 genomes]
rs7943429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47261600-47269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:47264600-47269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:47267000-47269400	Weak transcription	HSMMtube	muscle
5	chr11:47267400-47269600	Weak transcription	Aorta	Aorta
6	chr11:47267600-47269400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr11:47267600-47269400	Weak transcription	A549	lung
8	chr11:47267800-47269400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:47267800-47269400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:47267800-47269400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:47267800-47269400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:47267800-47269600	Weak transcription	Primary B cells from cord blood	blood
13	chr11:47267800-47269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:47268000-47269400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:47268400-47269600	Genic enhancers	Placenta	Placenta
16	chr11:47268400-47269600	Enhancers	Right Atrium	heart
17	chr11:47268400-47269600	Genic enhancers	Spleen	Spleen
18	chr11:47268600-47269400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr11:47268600-47269400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr11:47268600-47269400	Enhancers	Right Ventricle	heart
21	chr11:47268600-47269600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:47268600-47269600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:47268600-47269600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:47268600-47269600	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr11:47268600-47269600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
26	chr11:47268600-47269800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:47268600-47269800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:47268600-47269800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:47268600-47270000	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr11:47268600-47270000	Flanking Active TSS	Dnd41	blood
31	chr11:47268800-47269400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:47268800-47269400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:47268800-47269400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr11:47268800-47269400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:47268800-47269400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:47268800-47269400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
37	chr11:47268800-47269400	Enhancers	Fetal Lung	lung
38	chr11:47268800-47269400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
39	chr11:47268800-47269400	Enhancers	HMEC	breast
40	chr11:47268800-47269600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr11:47268800-47269600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr11:47268800-47269600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr11:47268800-47269600	Flanking Active TSS	Pancreas	Pancrea
44	chr11:47268800-47269600	Enhancers	Stomach Mucosa	stomach
45	chr11:47268800-47270000	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr11:47268800-47270000	Flanking Active TSS	Hela-S3	cervix
47	chr11:47269000-47269400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:47269000-47269400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr11:47269000-47269400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:47269000-47269400	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links