Variant report

Variant	rs2720289
Chromosome Location	chr12:50198935-50198936
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50188724..50191324-chr12:50196893..50199572,2	K562	blood:
2	chr12:50197457..50199102-chr12:50202144..50204971,2	K562	blood:
3	chr12:50135738..50138027-chr12:50197622..50200585,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BCDIN3D-1	chr12:50197705-50199173	NONHSAT028141

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11169158	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169159	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12305896	1.00[ASN][1000 genomes]
rs12313989	0.97[ASN][1000 genomes]
rs12316892	0.89[ASN][1000 genomes]
rs2603113	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2720288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741556	0.94[ASN][1000 genomes]
rs67453698	0.85[ASN][1000 genomes]
rs72644870	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72644871	0.95[ASN][1000 genomes]
rs897055	0.97[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
3	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
4	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:50183400-50200000	Strong transcription	Brain Hippocampus Middle	brain
8	chr12:50183400-50200000	Strong transcription	Brain Inferior Temporal Lobe	brain
9	chr12:50183400-50200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:50183400-50200200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr12:50183400-50200600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:50183400-50200600	Strong transcription	Fetal Brain Female	brain
13	chr12:50183400-50202200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:50183400-50202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:50183400-50202600	Strong transcription	NHLF	lung
16	chr12:50183800-50199800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:50184400-50200000	Strong transcription	Lung	lung
18	chr12:50184400-50200000	Strong transcription	Spleen	Spleen
19	chr12:50184400-50200200	Strong transcription	Brain Germinal Matrix	brain
20	chr12:50184400-50203200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:50184600-50199800	Strong transcription	Brain Anterior Caudate	brain
22	chr12:50184800-50199800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:50185000-50202400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:50185200-50200000	Strong transcription	Gastric	stomach
25	chr12:50185200-50200200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:50185200-50200200	Strong transcription	Fetal Thymus	thymus
27	chr12:50185200-50200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:50185600-50201200	Strong transcription	Fetal Stomach	stomach
29	chr12:50185800-50199800	Strong transcription	Placenta	Placenta
30	chr12:50185800-50200400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:50186200-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:50187000-50199800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:50187200-50203000	Strong transcription	Primary T cells from cord blood	blood
34	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:50188400-50200000	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr12:50188800-50199800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr12:50188800-50200200	Strong transcription	Thymus	Thymus
38	chr12:50189000-50200000	Strong transcription	NHEK	skin
39	chr12:50189200-50199600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:50189200-50214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:50189400-50200000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:50189800-50199600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:50189800-50200000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:50190000-50199200	Strong transcription	Aorta	Aorta
45	chr12:50190000-50200000	Strong transcription	Pancreas	Pancrea
46	chr12:50190200-50199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:50190200-50200000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:50190200-50200400	Strong transcription	Osteobl	bone
49	chr12:50190400-50199200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:50190400-50200400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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