Variant report

Variant	rs2509731
Chromosome Location	chr11:59555677-59555678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:59520935..59525781-chr11:59552803..59557885,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254477	Chromatin interaction
ENSG00000166900	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1144728	1.00[YRI][hapmap]
rs477945	1.00[AFR][1000 genomes]
rs478935	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs491671	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs493567	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs504954	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs515974	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs538323	1.00[AFR][1000 genomes]
rs539537	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs547093	1.00[AFR][1000 genomes]
rs554598	0.86[AFR][1000 genomes]
rs569031	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046086	chr11:59520424-59561455	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59524400-59557000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:59524600-59557400	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:59524600-59573800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:59525600-59557800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:59534400-59559600	Weak transcription	Fetal Brain Female	brain
6	chr11:59534600-59571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:59537600-59570400	Weak transcription	Fetal Kidney	kidney
8	chr11:59540800-59556200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr11:59540800-59559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:59541000-59560000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:59541000-59573600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr11:59541800-59559200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:59542200-59571400	Weak transcription	Thymus	Thymus
14	chr11:59542800-59557800	Weak transcription	Fetal Stomach	stomach
15	chr11:59543200-59557000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr11:59543200-59559200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:59544400-59573200	Weak transcription	Psoas Muscle	Psoas
18	chr11:59546000-59556600	Weak transcription	Brain Angular Gyrus	brain
19	chr11:59546000-59557800	Weak transcription	Brain Anterior Caudate	brain
20	chr11:59546000-59560800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:59546400-59568800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:59548400-59556200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:59551400-59572800	Weak transcription	Dnd41	blood
24	chr11:59551600-59573600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:59551600-59576600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:59551600-59577200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:59552000-59573000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr11:59553200-59556000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:59553800-59555800	Enhancers	NHDF-Ad	bronchial
30	chr11:59553800-59556400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr11:59554000-59555800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr11:59554000-59555800	Enhancers	HSMM	muscle
33	chr11:59554000-59556000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:59554000-59556000	Enhancers	Fetal Heart	heart
35	chr11:59554200-59555800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:59554200-59555800	Flanking Active TSS	Osteobl	bone
37	chr11:59554200-59563600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:59554200-59565200	Strong transcription	Primary T cells from cord blood	blood
39	chr11:59554200-59565600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:59554200-59565600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:59554400-59565600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr11:59554400-59569000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:59554600-59555800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:59554600-59555800	Genic enhancers	Gastric	stomach
45	chr11:59554600-59555800	Genic enhancers	Lung	lung
46	chr11:59554600-59564800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:59554600-59565200	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr11:59554600-59565800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:59554600-59569000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr11:59554800-59555800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links