Variant report

Variant	rs2620353
Chromosome Location	chr12:122405435-122405436
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	chr12:122396876..122400542-chr12:122404615..122407753,3	MCF-7	breast:
2	chr12:122403298..122406654-chr12:122407062..122410131,3	K562	blood:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1154513	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1169075	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1169077	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1169080	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1169085	0.84[ASN][1000 genomes]
rs1182927	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1185260	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1667580	0.86[ASN][1000 genomes]
rs1667583	0.86[ASN][1000 genomes]
rs1667584	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1678951	0.86[ASN][1000 genomes]
rs1678969	0.86[ASN][1000 genomes]
rs1916333	0.82[ASN][1000 genomes]
rs2247139	0.85[ASN][1000 genomes]
rs493519	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs693277	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs830116	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs830122	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs830126	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs853758	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs895958	0.86[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
2	chr12:122374000-122405600	Weak transcription	Adipose Nuclei	Adipose
3	chr12:122375800-122415800	Weak transcription	Liver	Liver
4	chr12:122376000-122413000	Weak transcription	Aorta	Aorta
5	chr12:122377400-122406200	Weak transcription	Thymus	Thymus
6	chr12:122380800-122405800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:122381000-122405800	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:122391400-122410800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:122391600-122405600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:122391800-122410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:122394200-122407600	Weak transcription	Brain Angular Gyrus	brain
13	chr12:122394200-122411000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:122394200-122411200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:122396000-122408000	Weak transcription	Fetal Intestine Small	intestine
16	chr12:122396600-122408200	Weak transcription	Fetal Brain Female	brain
17	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:122396800-122410800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:122397200-122406000	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:122397200-122408400	Weak transcription	Brain Substantia Nigra	brain
21	chr12:122397600-122406000	Weak transcription	Esophagus	oesophagus
22	chr12:122398800-122406200	Weak transcription	Fetal Thymus	thymus
23	chr12:122399000-122411000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:122399000-122411000	Weak transcription	Gastric	stomach
25	chr12:122400200-122408200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:122401400-122408200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:122402000-122405800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:122402000-122405800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:122402000-122406000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:122402000-122408800	Weak transcription	Pancreas	Pancrea
31	chr12:122402000-122412400	Weak transcription	Ovary	ovary
32	chr12:122402000-122412800	Weak transcription	Spleen	Spleen
33	chr12:122402800-122407200	Weak transcription	Placenta	Placenta
34	chr12:122403000-122408400	Weak transcription	NH-A	brain
35	chr12:122403400-122405600	Weak transcription	Fetal Stomach	stomach
36	chr12:122403400-122405800	Weak transcription	NHLF	lung
37	chr12:122403400-122406800	Weak transcription	Fetal Lung	lung
38	chr12:122403400-122407600	Weak transcription	A549	lung
39	chr12:122403400-122410800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:122403400-122411000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:122403400-122417200	Weak transcription	NHDF-Ad	bronchial
42	chr12:122403600-122407800	Weak transcription	HUVEC	blood vessel
43	chr12:122403600-122408200	Weak transcription	Fetal Kidney	kidney
44	chr12:122403800-122412400	Weak transcription	HSMM	muscle
45	chr12:122403800-122412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:122404000-122405800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:122404000-122406000	Weak transcription	Osteobl	bone
48	chr12:122404000-122406400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:122404000-122410000	Weak transcription	HMEC	breast
50	chr12:122404000-122410800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links