Variant report

Variant	rs28664930
Chromosome Location	chr12:123895197-123895198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123871220..123876084-chr12:123892723..123900288,8	K562	blood:
2	chr12:123891872..123893382-chr12:123894921..123897058,2	MCF-7	breast:
3	chr12:123894977..123897408-chr12:124087588..124090570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction
ENSG00000111364	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10846516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap]
rs11057239	1.00[CEU][hapmap]
rs11057252	1.00[CEU][hapmap]
rs11057265	1.00[CEU][hapmap]
rs11057278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28553365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs28624763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28690392	0.88[EUR][1000 genomes]
rs28698461	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs28828722	0.83[EUR][1000 genomes]
rs28875264	0.88[EUR][1000 genomes]
rs3881293	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55932027	0.88[EUR][1000 genomes]
rs7296458	1.00[MEX][hapmap]
rs73216930	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73216932	1.00[EUR][1000 genomes]
rs73233508	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv975551	chr12:123888322-123897046	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
2	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:123883200-123895400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:123883800-123895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:123884200-123895200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:123886000-123895200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:123886000-123895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:123886200-123895200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:123886200-123895200	Strong transcription	Fetal Muscle Leg	muscle
11	chr12:123886200-123895200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:123886200-123895200	Strong transcription	Dnd41	blood
13	chr12:123886200-123895400	Strong transcription	Fetal Brain Female	brain
14	chr12:123886400-123895200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:123886400-123895200	Strong transcription	Spleen	Spleen
16	chr12:123886400-123895200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:123886400-123895200	Strong transcription	NHLF	lung
18	chr12:123886400-123895400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:123886400-123895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:123886400-123895400	Strong transcription	Thymus	Thymus
21	chr12:123886600-123895200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:123887000-123895200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:123887000-123897600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:123887200-123895200	Strong transcription	Brain Cingulate Gyrus	brain
25	chr12:123887200-123895200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:123887400-123895600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:123888000-123896200	Strong transcription	Lung	lung
28	chr12:123888200-123895200	Strong transcription	Brain Hippocampus Middle	brain
29	chr12:123888200-123895200	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:123889200-123895200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:123889600-123902600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:123889600-123917000	Weak transcription	K562	blood
33	chr12:123889800-123902800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:123890200-123895800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:123890200-123896400	Weak transcription	Primary B cells from cord blood	blood
36	chr12:123890800-123917200	Weak transcription	Fetal Kidney	kidney
37	chr12:123891000-123895400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:123891200-123920400	Weak transcription	Psoas Muscle	Psoas
39	chr12:123891400-123908600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:123891600-123919800	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:123891600-123920000	Weak transcription	Small Intestine	intestine
42	chr12:123891800-123900000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:123892000-123899600	Weak transcription	Primary T cells from cord blood	blood
44	chr12:123892000-123899600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:123892000-123903800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:123892000-123911400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:123892200-123895200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:123892200-123895400	Strong transcription	Fetal Stomach	stomach
49	chr12:123892200-123897000	Weak transcription	Ovary	ovary
50	chr12:123892200-123901200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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