Variant report

Variant	rs559298
Chromosome Location	chr11:65998757-65998758
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	chr11:65998063..65999977-chr11:66024495..66026348,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1190945	0.83[AFR][1000 genomes]
rs1203551	0.83[AFR][1000 genomes]
rs1203552	0.83[AFR][1000 genomes]
rs1203801	1.00[YRI][hapmap]
rs1300706	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1783732	1.00[YRI][hapmap]
rs2452687	1.00[YRI][hapmap]
rs3017606	0.80[AFR][1000 genomes]
rs4523703	0.83[YRI][hapmap]
rs471709	1.00[YRI][hapmap]
rs477001	1.00[YRI][hapmap]
rs496438	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs505412	0.84[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs505642	1.00[YRI][hapmap]
rs510398	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs512316	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs515778	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs519911	1.00[YRI][hapmap]
rs527279	1.00[YRI][hapmap]
rs541954	1.00[YRI][hapmap]
rs547282	1.00[YRI][hapmap]
rs555527	1.00[YRI][hapmap]
rs555826	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs55640200	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55701638	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55982441	1.00[ASN][1000 genomes]
rs561199	1.00[YRI][hapmap]
rs561869	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs568423	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs571368	0.84[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs572697	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs572827	0.96[EUR][1000 genomes]
rs581247	0.83[AFR][1000 genomes]
rs72932632	1.00[ASN][1000 genomes]
rs72936614	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72936653	1.00[ASN][1000 genomes]
rs72936669	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72936679	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72936683	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72936686	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72936687	1.00[EUR][1000 genomes]
rs72936689	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72938506	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs948358	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65961400-66011200	Weak transcription	Psoas Muscle	Psoas
2	chr11:65976600-66006000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:65977400-66010600	Strong transcription	Fetal Stomach	stomach
4	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:65979800-66001200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:65984600-66024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:65984800-66000400	Weak transcription	HMEC	breast
8	chr11:65985200-65998800	Weak transcription	NHDF-Ad	bronchial
9	chr11:65985800-66017800	Weak transcription	Fetal Heart	heart
10	chr11:65987800-66003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:65988200-66001200	Weak transcription	Small Intestine	intestine
12	chr11:65988800-65998800	Weak transcription	Colonic Mucosa	Colon
13	chr11:65989600-66024200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:65990000-66002600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:65990200-65999200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:65990200-65999200	Weak transcription	Stomach Mucosa	stomach
17	chr11:65990200-66003000	Weak transcription	HepG2	liver
18	chr11:65990200-66007600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr11:65990200-66019800	Strong transcription	Primary T cells from cord blood	blood
20	chr11:65990400-66009200	Weak transcription	K562	blood
21	chr11:65990600-66003000	Weak transcription	Fetal Kidney	kidney
22	chr11:65990600-66015800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:65990600-66018400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:65990800-66008600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:65990800-66009200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr11:65990800-66018600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:65991000-66000000	Weak transcription	Dnd41	blood
28	chr11:65991000-66000600	Strong transcription	Adipose Nuclei	Adipose
29	chr11:65991000-66015400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:65991200-65998800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:65991200-66012400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:65991200-66018600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:65991200-66018600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:65991600-66008200	Strong transcription	Primary B cells from cord blood	blood
35	chr11:65991600-66012800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:65991600-66018400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:65991600-66018400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:65991800-65998800	Strong transcription	Fetal Thymus	thymus
39	chr11:65991800-66004000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:65991800-66005400	Strong transcription	Thymus	Thymus
41	chr11:65991800-66018400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:65992800-66009600	Weak transcription	HUVEC	blood vessel
43	chr11:65993800-66004000	Strong transcription	Primary hematopoietic stem cells	blood
44	chr11:65993800-66018400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr11:65994400-66015200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:65994400-66018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:65994600-66013200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr11:65994600-66013800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:65994600-66018600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:65994800-66002800	Strong transcription	NH-A	brain

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