Variant report

Variant	rs59975561
Chromosome Location	chr12:123884515-123884516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123882533..123885309-chr12:123899138..123901801,2	MCF-7	breast:
2	chr12:123879767..123882314-chr12:123882742..123884960,2	MCF-7	breast:
3	chr12:123883208..123885553-chr12:123941974..123944091,2	MCF-7	breast:
4	chr12:123847504..123849899-chr12:123882139..123884524,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139697	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs57277091	0.85[AFR][1000 genomes]
rs57739745	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73410296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73421386	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73423314	0.85[AFR][1000 genomes]

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	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875000-123886400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123875200-123884600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:123875400-123884600	Strong transcription	Primary T cells from cord blood	blood
5	chr12:123875600-123884600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:123875600-123885400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
9	chr12:123875800-123884600	Strong transcription	Placenta Amnion	Placenta Amnion
10	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:123876200-123885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:123876400-123884600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
14	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:123876800-123885400	Strong transcription	Fetal Brain Female	brain
16	chr12:123876800-123887600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:123877000-123885000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:123877000-123885600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:123877400-123889000	Weak transcription	Fetal Heart	heart
20	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:123878200-123884600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:123879000-123884600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:123879600-123884600	Strong transcription	Dnd41	blood
24	chr12:123881400-123886400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:123881600-123884800	Strong transcription	Fetal Intestine Large	intestine
26	chr12:123881600-123887200	Weak transcription	Small Intestine	intestine
27	chr12:123881600-123888200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:123881600-123888400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:123881600-123888600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:123881600-123889000	Weak transcription	Fetal Brain Male	brain
31	chr12:123881800-123886800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:123881800-123887200	Weak transcription	Primary B cells from cord blood	blood
33	chr12:123881800-123888800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:123881800-123889000	Weak transcription	Fetal Kidney	kidney
35	chr12:123882000-123886800	Weak transcription	HepG2	liver
36	chr12:123882000-123888600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:123883200-123895400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:123883400-123885800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:123883400-123886400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:123883400-123886400	Weak transcription	Hela-S3	cervix
42	chr12:123883800-123884600	Strong transcription	Liver	Liver
43	chr12:123883800-123894200	Strong transcription	HUVEC	blood vessel
44	chr12:123883800-123895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:123884000-123886400	Weak transcription	NHLF	lung
46	chr12:123884000-123886600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:123884000-123886600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr12:123884000-123886600	Strong transcription	Fetal Stomach	stomach
49	chr12:123884000-123887800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:123884000-123888800	Weak transcription	Psoas Muscle	Psoas

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