Variant report

Variant	rs11039228
Chromosome Location	chr11:47436531-47436532
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47202498..47205214-chr11:47434945..47437570,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MADD-4	chr11:47436328-47436646	NONHSAT021242

Variant related genes	Relation type
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1017594	1.00[AFR][1000 genomes]
rs10466401	1.00[AFR][1000 genomes]
rs10742808	1.00[AFR][1000 genomes]
rs10769261	1.00[AFR][1000 genomes]
rs10769269	1.00[AFR][1000 genomes]
rs10838701	1.00[AFR][1000 genomes]
rs11039196	1.00[AFR][1000 genomes]
rs11602132	1.00[AFR][1000 genomes]
rs2020057	1.00[AFR][1000 genomes]
rs2084541	1.00[AFR][1000 genomes]
rs2868447	1.00[AFR][1000 genomes]
rs2868603	1.00[AFR][1000 genomes]
rs4519056	1.00[AFR][1000 genomes]
rs4752826	1.00[AFR][1000 genomes]
rs4752831	1.00[AFR][1000 genomes]
rs4752841	1.00[AFR][1000 genomes]
rs4752982	1.00[AFR][1000 genomes]
rs4752985	1.00[AFR][1000 genomes]
rs4752989	1.00[AFR][1000 genomes]
rs4752991	1.00[AFR][1000 genomes]
rs4752995	1.00[AFR][1000 genomes]
rs6485754	1.00[AFR][1000 genomes]
rs7105005	1.00[AFR][1000 genomes]
rs7119799	1.00[AFR][1000 genomes]
rs7932148	1.00[AFR][1000 genomes]
rs7934846	1.00[AFR][1000 genomes]
rs7951044	1.00[AFR][1000 genomes]
rs963331	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
9	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 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	chr11:47431000-47439200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:47431000-47440000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:47431000-47442000	Weak transcription	Primary B cells from cord blood	blood
4	chr11:47431200-47437600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:47431200-47439000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:47431200-47439800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr11:47431200-47440600	Weak transcription	Small Intestine	intestine
8	chr11:47431200-47447200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:47431400-47436600	Weak transcription	Psoas Muscle	Psoas
10	chr11:47431400-47440400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:47431600-47437400	Strong transcription	Fetal Intestine Small	intestine
12	chr11:47431600-47437800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:47431600-47439000	Weak transcription	K562	blood
14	chr11:47431600-47439600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr11:47431600-47439800	Weak transcription	GM12878-XiMat	blood
16	chr11:47431600-47440200	Genic enhancers	Right Ventricle	heart
17	chr11:47431600-47440400	Weak transcription	Fetal Kidney	kidney
18	chr11:47431600-47446400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:47431800-47437000	Weak transcription	Right Atrium	heart
20	chr11:47431800-47438800	Genic enhancers	Fetal Muscle Leg	muscle
21	chr11:47431800-47440400	Genic enhancers	Placenta	Placenta
22	chr11:47431800-47440800	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr11:47432000-47437200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:47432000-47437400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:47432200-47437200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:47432200-47438600	Genic enhancers	HMEC	breast
27	chr11:47432200-47446400	Strong transcription	Thymus	Thymus
28	chr11:47432400-47437200	Strong transcription	Fetal Intestine Large	intestine
29	chr11:47432400-47437200	Strong transcription	Ovary	ovary
30	chr11:47432400-47440800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:47432400-47445800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:47432400-47446400	Weak transcription	Fetal Brain Male	brain
33	chr11:47432600-47437000	Strong transcription	Gastric	stomach
34	chr11:47432600-47437200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:47432600-47437600	Weak transcription	Stomach Mucosa	stomach
36	chr11:47432600-47437800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:47432600-47445800	Strong transcription	Brain Anterior Caudate	brain
38	chr11:47432600-47446400	Strong transcription	Fetal Brain Female	brain
39	chr11:47432800-47437400	Genic enhancers	HSMM	muscle
40	chr11:47432800-47446000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:47432800-47446200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:47432800-47446400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:47433200-47446200	Strong transcription	Fetal Thymus	thymus
44	chr11:47433400-47437000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:47433400-47438600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:47433400-47445800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:47433600-47437400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:47433600-47438000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:47433800-47436800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:47434000-47436800	Strong transcription	Left Ventricle	heart

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