Variant report

Variant	rs12227707
Chromosome Location	chr12:59262269-59262270
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	chr12:59259480..59262416-chr12:59311926..59314083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10877176	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877177	0.81[YRI][hapmap]
rs10877178	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10877179	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877180	0.93[CHB][hapmap]
rs11172770	0.91[EUR][1000 genomes]
rs11172772	0.93[EUR][1000 genomes]
rs11172789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12367032	0.93[EUR][1000 genomes]
rs6581221	0.93[EUR][1000 genomes]
rs7305422	0.84[EUR][1000 genomes]
rs7979355	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv3440532	chr12:59244734-59266539	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59243200-59263600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:59251000-59266400	Weak transcription	Esophagus	oesophagus
3	chr12:59251800-59263400	Weak transcription	NHEK	skin
4	chr12:59253000-59270200	Weak transcription	Fetal Brain Male	brain
5	chr12:59253400-59265400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:59254600-59268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:59254800-59266400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:59254800-59267000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:59255000-59265400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:59255000-59267400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:59255200-59263400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:59255400-59267000	Weak transcription	Pancreas	Pancrea
13	chr12:59256200-59266400	Weak transcription	Left Ventricle	heart
14	chr12:59256400-59262400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:59256600-59266400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:59256800-59263600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:59257000-59270800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:59257400-59264600	Strong transcription	NHDF-Ad	bronchial
19	chr12:59257600-59263400	Weak transcription	A549	lung
20	chr12:59257600-59266600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:59257800-59262600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:59257800-59265400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:59258000-59266400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:59258000-59266800	Weak transcription	Psoas Muscle	Psoas
25	chr12:59258000-59267000	Weak transcription	Gastric	stomach
26	chr12:59258000-59267200	Weak transcription	Aorta	Aorta
27	chr12:59258600-59267000	Weak transcription	Lung	lung
28	chr12:59258800-59263200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:59258800-59265400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:59258800-59266400	Weak transcription	Colonic Mucosa	Colon
31	chr12:59258800-59266400	Weak transcription	Right Ventricle	heart
32	chr12:59258800-59266600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:59258800-59266800	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:59258800-59267400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:59259000-59262600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:59259000-59266600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:59259200-59265400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:59259200-59270200	Strong transcription	HMEC	breast
39	chr12:59259800-59267200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:59260000-59263800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:59260000-59267400	Weak transcription	Brain Substantia Nigra	brain
42	chr12:59260200-59266400	Weak transcription	Placenta	Placenta
43	chr12:59260400-59267000	Weak transcription	Fetal Stomach	stomach
44	chr12:59260400-59267200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:59260400-59267200	Weak transcription	Fetal Intestine Small	intestine
46	chr12:59260400-59270200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:59260600-59263000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:59260600-59284200	Strong transcription	HUVEC	blood vessel
49	chr12:59260800-59265600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:59260800-59267600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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