Variant report

Variant	rs11668239
Chromosome Location	chr19:42583493-42583494
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	chr19:42362802..42365669-chr19:42579542..42583856,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10425682	1.00[CHD][hapmap]
rs11083643	1.00[CHD][hapmap];1.00[LWK][hapmap]
rs11669918	1.00[CEU][hapmap];1.00[LWK][hapmap]
rs11671088	1.00[LWK][hapmap]
rs11672172	1.00[CEU][hapmap]
rs12460885	1.00[LWK][hapmap]
rs12609687	1.00[CHD][hapmap]
rs12610025	1.00[LWK][hapmap]
rs12976997	1.00[CHD][hapmap]
rs12978003	1.00[CEU][hapmap];1.00[LWK][hapmap]
rs12985559	1.00[CHD][hapmap];1.00[LWK][hapmap]
rs2290694	1.00[CHD][hapmap]
rs2303797	1.00[CEU][hapmap];1.00[LWK][hapmap]
rs28364793	1.00[LWK][hapmap]
rs34343924	1.00[LWK][hapmap]
rs34578730	1.00[CHD][hapmap]
rs3745226	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs3745227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap]
rs3745228	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs9676263	1.00[LWK][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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer 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 miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv911783	chr19:42575462-42624662	Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 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	chr19:42581400-42584000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:42582000-42583600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:42582000-42583800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:42582000-42584400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:42582000-42585400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:42582000-42587800	Weak transcription	Fetal Kidney	kidney
7	chr19:42582000-42590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:42582200-42583600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr19:42582200-42584000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:42582200-42584000	Enhancers	NH-A	brain
11	chr19:42582200-42585000	Weak transcription	Psoas Muscle	Psoas
12	chr19:42582200-42585600	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:42582200-42586600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr19:42582200-42587200	Strong transcription	Fetal Muscle Leg	muscle
15	chr19:42582200-42588400	Strong transcription	Lung	lung
16	chr19:42582200-42596000	Weak transcription	Right Atrium	heart
17	chr19:42582200-42597800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:42582400-42583800	Genic enhancers	A549	lung
19	chr19:42582400-42584000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:42582400-42584000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:42582400-42584000	Genic enhancers	NHEK	skin
22	chr19:42582400-42584800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:42582400-42584800	Weak transcription	Small Intestine	intestine
24	chr19:42582400-42585000	Weak transcription	Stomach Mucosa	stomach
25	chr19:42582400-42585400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:42582400-42585600	Strong transcription	Fetal Intestine Large	intestine
27	chr19:42582400-42585600	Genic enhancers	Spleen	Spleen
28	chr19:42582400-42585800	Strong transcription	Fetal Intestine Small	intestine
29	chr19:42582400-42586000	Strong transcription	Liver	Liver
30	chr19:42582400-42586200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:42582400-42586200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:42582400-42586400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:42582400-42586400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr19:42582400-42586400	Strong transcription	Primary T cells from cord blood	blood
35	chr19:42582400-42586600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:42582400-42586600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:42582400-42586600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:42582400-42586600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr19:42582400-42586600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr19:42582400-42586600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:42582400-42586600	Strong transcription	Brain Angular Gyrus	brain
42	chr19:42582400-42586600	Strong transcription	Brain Hippocampus Middle	brain
43	chr19:42582400-42586600	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr19:42582400-42586600	Strong transcription	Fetal Thymus	thymus
45	chr19:42582400-42586600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr19:42582400-42588200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:42582400-42588400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:42582400-42588800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:42582400-42588800	Strong transcription	Fetal Stomach	stomach
50	chr19:42582400-42592800	Weak transcription	HSMMtube	muscle

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