Variant report

Variant	rs12423154
Chromosome Location	chr12:118559692-118559693
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr12:118559486-118559807	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr12:118559497-118559768	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:118497477..118500466-chr12:118559121..118561956,3	MCF-7	breast:
2	chr12:118558694..118561471-chr12:118568462..118574858,6	MCF-7	breast:
3	chr12:118557596..118560350-chr12:118572704..118574934,3	MCF-7	breast:
4	chr12:118498692..118501195-chr12:118558625..118560440,2	MCF-7	breast:
5	chr12:118539824..118542719-chr12:118557194..118560231,3	MCF-7	breast:

No data

Variant related genes	Relation type
VSIG10	TF binding region
ENSG00000176871	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000089220	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12423959	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017414	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2936840	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3847652	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56070243	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61943518	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61943519	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943521	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73217996	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs795476	0.82[CHB][hapmap]
rs7956285	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961197	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970036	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv560389	chr12:118502467-118564087	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv899546	chr12:118515230-118563982	Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118542400-118562400	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:118542400-118569400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:118542600-118569400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:118542600-118572800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:118542600-118573400	Weak transcription	Primary T cells from cord blood	blood
6	chr12:118545400-118569600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:118546400-118569400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:118548600-118563400	Weak transcription	Left Ventricle	heart
9	chr12:118552400-118561400	Weak transcription	Fetal Stomach	stomach
10	chr12:118552800-118572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:118552800-118573400	Weak transcription	Aorta	Aorta
12	chr12:118553000-118573000	Weak transcription	Fetal Brain Female	brain
13	chr12:118554200-118560400	Weak transcription	Spleen	Spleen
14	chr12:118554200-118561400	Weak transcription	Pancreas	Pancrea
15	chr12:118554400-118566000	Weak transcription	Small Intestine	intestine
16	chr12:118554800-118564000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:118557800-118564000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:118558200-118564000	Enhancers	HepG2	liver
19	chr12:118558800-118559800	Enhancers	Ovary	ovary
20	chr12:118558800-118564000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:118558800-118572800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:118559000-118559800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:118559000-118561000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:118559000-118565600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:118559000-118569200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:118559200-118559800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr12:118559200-118560800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr12:118559200-118564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:118559200-118564000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:118559200-118566600	Weak transcription	Fetal Lung	lung
31	chr12:118559200-118567200	Weak transcription	Brain Angular Gyrus	brain
32	chr12:118559200-118569400	Weak transcription	Adipose Nuclei	Adipose
33	chr12:118559200-118569400	Weak transcription	Dnd41	blood
34	chr12:118559200-118569600	Weak transcription	GM12878-XiMat	blood
35	chr12:118559200-118569800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:118559200-118570000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:118559200-118572600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:118559200-118572600	Weak transcription	NHEK	skin
39	chr12:118559200-118572800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:118559200-118573000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:118559200-118573000	Weak transcription	Fetal Kidney	kidney
42	chr12:118559200-118573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:118559200-118573400	Weak transcription	Fetal Intestine Small	intestine
44	chr12:118559400-118559800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr12:118559400-118559800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr12:118559400-118560600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:118559400-118561200	Weak transcription	Liver	Liver
48	chr12:118559400-118561400	Weak transcription	Stomach Mucosa	stomach
49	chr12:118559400-118562200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr12:118559400-118562200	Weak transcription	K562	blood

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