Variant report

Variant	rs3024985
Chromosome Location	chr12:57488707-57488708
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	chr12:57487207..57489372-chr12:57634263..57636332,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRP1-1	chr12:57488595-57489256	NONHSAT028876

Variant related genes	Relation type
ENSG00000185633	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1800160	1.00[AFR][1000 genomes]
rs1800184	1.00[AFR][1000 genomes]
rs3024981	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35292422	1.00[AFR][1000 genomes]
rs3782327	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7979451	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57483800-57492000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:57484000-57498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:57484400-57490800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:57484400-57491000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:57484600-57488800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:57484600-57488800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:57484600-57489000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:57484800-57488800	Genic enhancers	Placenta	Placenta
9	chr12:57484800-57489000	Genic enhancers	Placenta Amnion	Placenta Amnion
10	chr12:57484800-57489400	Genic enhancers	Primary T cells from cord blood	blood
11	chr12:57484800-57490800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:57485000-57489000	Genic enhancers	Liver	Liver
13	chr12:57485000-57489400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:57485000-57490800	Genic enhancers	Fetal Thymus	thymus
15	chr12:57485000-57491000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:57485000-57491000	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr12:57485000-57491400	Strong transcription	Aorta	Aorta
18	chr12:57485200-57488800	Genic enhancers	Fetal Muscle Leg	muscle
19	chr12:57485200-57488800	Genic enhancers	Fetal Stomach	stomach
20	chr12:57485200-57489800	Strong transcription	HepG2	liver
21	chr12:57485200-57490000	Genic enhancers	NH-A	brain
22	chr12:57485400-57488800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:57485400-57491000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:57485400-57491200	Strong transcription	Fetal Intestine Large	intestine
25	chr12:57485600-57489000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:57485600-57490600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
27	chr12:57485800-57488800	Genic enhancers	Adipose Nuclei	Adipose
28	chr12:57485800-57490000	Strong transcription	Gastric	stomach
29	chr12:57486000-57489000	Genic enhancers	HSMMtube	muscle
30	chr12:57486000-57489800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:57486200-57503600	Weak transcription	Fetal Brain Male	brain
32	chr12:57486400-57488800	Enhancers	Primary B cells from cord blood	blood
33	chr12:57486600-57489000	Genic enhancers	Colon Smooth Muscle	Colon
34	chr12:57486600-57503800	Weak transcription	Brain Substantia Nigra	brain
35	chr12:57486800-57488800	Genic enhancers	H1 Cell Line	embryonic stem cell
36	chr12:57486800-57491200	Weak transcription	Hela-S3	cervix
37	chr12:57487000-57488800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:57487200-57488800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
39	chr12:57487200-57488800	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:57487200-57489400	Genic enhancers	Lung	lung
41	chr12:57487200-57490400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:57487200-57491000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:57487200-57491000	Genic enhancers	Esophagus	oesophagus
44	chr12:57487200-57491000	Genic enhancers	NHEK	skin
45	chr12:57487400-57488800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr12:57487400-57488800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:57487600-57489000	Enhancers	NHDF-Ad	bronchial
48	chr12:57487600-57490800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:57487600-57491000	Genic enhancers	HMEC	breast
50	chr12:57487600-57501400	Weak transcription	Right Atrium	heart

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