Variant report

Variant	rs2288559
Chromosome Location	chr15:52446464-52446465
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52399033..52401663-chr15:52446197..52448357,2	MCF-7	breast:
2	chr15:52446218..52447744-chr15:52470239..52472909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10851508	0.87[ASN][1000 genomes]
rs2414129	1.00[CEU][hapmap]
rs3751603	0.87[GIH][hapmap]
rs3794545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7166828	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:52423000-52458200	Weak transcription	Dnd41	blood
3	chr15:52429000-52447200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:52429200-52447400	Strong transcription	Primary T cells from cord blood	blood
5	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
6	chr15:52430200-52446600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:52430200-52457800	Weak transcription	Fetal Intestine Large	intestine
8	chr15:52431400-52446600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:52432200-52453800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:52432200-52455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:52432200-52455200	Weak transcription	Colonic Mucosa	Colon
12	chr15:52435000-52446600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:52436800-52457200	Weak transcription	GM12878-XiMat	blood
14	chr15:52437200-52456800	Weak transcription	HSMM	muscle
15	chr15:52437400-52446800	Weak transcription	HSMMtube	muscle
16	chr15:52437400-52454000	Weak transcription	NH-A	brain
17	chr15:52437400-52454400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:52437800-52463600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:52438000-52455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:52438800-52446600	Strong transcription	Thymus	Thymus
21	chr15:52439200-52463600	Weak transcription	NHEK	skin
22	chr15:52439600-52454800	Weak transcription	NHDF-Ad	bronchial
23	chr15:52441000-52453800	Weak transcription	NHLF	lung
24	chr15:52441000-52457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:52442000-52455200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:52442000-52463600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:52442000-52463600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:52442200-52447200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:52442200-52447200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:52442200-52454800	Weak transcription	Fetal Intestine Small	intestine
31	chr15:52442200-52455800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
34	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:52442400-52457200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:52442400-52457200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:52442400-52457800	Weak transcription	Adipose Nuclei	Adipose
38	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:52442600-52470400	Weak transcription	HMEC	breast
40	chr15:52442800-52447000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:52442800-52454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
43	chr15:52443400-52455400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:52443600-52453800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:52443800-52446800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:52443800-52451000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:52443800-52451400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:52443800-52451600	Weak transcription	Hela-S3	cervix
49	chr15:52443800-52453600	Weak transcription	Spleen	Spleen
50	chr15:52443800-52455200	Weak transcription	Right Ventricle	heart

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