Variant report

Variant	rs55946424
Chromosome Location	chr12:12687417-12687418
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12684001..12705444-chr12:12707828..12718639,50	MCF-7	breast:
2	chr12:12602118..12604673-chr12:12687247..12689420,2	MCF-7	breast:
3	chr12:12677909..12679570-chr12:12685352..12687736,2	MCF-7	breast:
4	chr12:12685312..12688917-chr12:12690468..12693651,8	MCF-7	breast:
5	chr12:12686997..12688577-chr12:12699822..12702095,2	K562	blood:
6	chr12:12681668..12683344-chr12:12686468..12688798,2	MCF-7	breast:
7	chr12:12676154..12677988-chr12:12685954..12688802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11830917	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16908222	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4237940	0.87[ASN][1000 genomes]
rs4763837	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763838	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279058	1.00[ASN][1000 genomes]
rs58443254	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60909736	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73063452	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73063453	0.88[AMR][1000 genomes];1.00[ASN][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	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv523022	chr12:12673551-12688181	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12664000-12690400	Weak transcription	NHLF	lung
2	chr12:12672800-12691200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:12673000-12690200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:12674200-12691200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:12681200-12688000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:12681400-12693600	Weak transcription	Lung	lung
7	chr12:12682200-12691400	Weak transcription	Adipose Nuclei	Adipose
8	chr12:12682200-12693000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr12:12682400-12689000	Enhancers	Fetal Intestine Small	intestine
10	chr12:12683400-12693600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:12683800-12688800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:12685000-12692600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:12685200-12688600	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr12:12685400-12688200	Enhancers	Duodenum Mucosa	Duodenum
15	chr12:12685400-12688200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr12:12685400-12688600	Enhancers	Fetal Intestine Large	intestine
17	chr12:12685400-12689000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:12685400-12689600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr12:12685600-12687600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:12685600-12687600	Enhancers	Left Ventricle	heart
21	chr12:12685600-12687600	Enhancers	Pancreas	Pancrea
22	chr12:12685600-12688200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:12685600-12688800	Enhancers	Fetal Muscle Leg	muscle
24	chr12:12685800-12689200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr12:12686000-12687600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr12:12686200-12687600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr12:12686200-12687600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:12686200-12687600	Enhancers	Fetal Lung	lung
29	chr12:12686200-12687600	Enhancers	Ovary	ovary
30	chr12:12686200-12687600	Enhancers	A549	lung
31	chr12:12686200-12688200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:12686200-12688200	Enhancers	Brain Angular Gyrus	brain
33	chr12:12686200-12688200	Enhancers	Brain Substantia Nigra	brain
34	chr12:12686200-12688200	Enhancers	Right Atrium	heart
35	chr12:12686200-12688600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:12686200-12689000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr12:12686200-12689600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:12686400-12687600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr12:12686400-12687600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:12686400-12687600	Enhancers	Gastric	stomach
41	chr12:12686400-12687800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:12686400-12687800	Enhancers	Stomach Mucosa	stomach
43	chr12:12686400-12688200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:12686400-12688200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:12686400-12688200	Enhancers	Small Intestine	intestine
46	chr12:12686600-12687800	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr12:12686600-12692200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:12686600-12693600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:12686600-12701000	Weak transcription	HSMM	muscle
50	chr12:12686600-12703200	Weak transcription	NH-A	brain

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