Variant report

Variant	rs55826938
Chromosome Location	chr12:122328102-122328103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122212415..122216174-chr12:122326415..122328726,3	K562	blood:
2	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
3	chr12:122213395..122216201-chr12:122325531..122328146,2	MCF-7	breast:
4	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
5	chr12:122214229..122218603-chr12:122325636..122328202,4	MCF-7	breast:
6	chr12:122326753..122329169-chr12:122336409..122338553,2	K562	blood:
7	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
8	chr12:122325172..122329151-chr12:122329541..122333817,7	MCF-7	breast:
9	chr12:122063686..122066969-chr12:122326410..122329127,3	K562	blood:
10	chr12:122212254..122213915-chr12:122326858..122328726,2	K562	blood:
11	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
12	chr12:122326336..122328188-chr12:122688489..122691049,2	MCF-7	breast:
13	chr12:122326249..122328617-chr12:122709300..122711997,3	K562	blood:
14	chr12:122325289..122328252-chr12:122355129..122358130,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000188735	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000176383	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000182500	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10840625	0.82[ASN][1000 genomes]
rs1168658	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1168661	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12578258	0.81[EUR][1000 genomes]
rs12579730	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12817002	0.88[ASN][1000 genomes]
rs14259	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1720066	0.86[EUR][1000 genomes]
rs1720068	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2272135	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2442439	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2688409	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2707061	0.92[ASN][1000 genomes]
rs34506529	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34930953	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35252940	0.81[EUR][1000 genomes]
rs3741591	0.88[ASN][1000 genomes]
rs3825172	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4069666	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4760108	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs482421	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs483416	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs508395	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56177852	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58379261	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59517025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71456716	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs71456717	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7309105	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313748	0.81[EUR][1000 genomes]
rs7969647	0.88[ASN][1000 genomes]
rs876934	0.94[AMR][1000 genomes];0.95[EUR][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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122325800-122328200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:122325800-122328600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:122326200-122328200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr12:122326600-122328800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:122326800-122328200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr12:122327000-122328200	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr12:122327000-122328400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:122327000-122328400	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr12:122327200-122328200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:122327200-122328200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr12:122327200-122328200	Flanking Active TSS	Rectal Smooth Muscle	rectum
12	chr12:122327200-122328200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr12:122327200-122328200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr12:122327200-122328200	Flanking Active TSS	Dnd41	blood
15	chr12:122327200-122328200	Flanking Active TSS	Osteobl	bone
16	chr12:122327400-122328200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:122327400-122328200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr12:122327400-122328200	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr12:122327400-122328200	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr12:122327400-122328200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr12:122327400-122328200	Enhancers	Spleen	Spleen
22	chr12:122327400-122328200	Flanking Active TSS	Hela-S3	cervix
23	chr12:122327400-122328200	Flanking Active TSS	HepG2	liver
24	chr12:122327400-122328200	Flanking Active TSS	NH-A	brain
25	chr12:122327400-122328200	Flanking Active TSS	NHEK	skin
26	chr12:122327400-122328400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:122327400-122333000	Weak transcription	Aorta	Aorta
28	chr12:122327400-122340800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:122327600-122328200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:122327600-122328200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:122327600-122328200	Enhancers	Placenta	Placenta
32	chr12:122327600-122328200	Flanking Active TSS	GM12878-XiMat	blood
33	chr12:122327600-122328400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:122327600-122328400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:122327600-122328400	Enhancers	Lung	lung
36	chr12:122327600-122328800	Enhancers	Primary B cells from peripheral blood	blood
37	chr12:122327600-122328800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:122327600-122331600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:122327600-122331600	Weak transcription	Esophagus	oesophagus
40	chr12:122327600-122340600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:122327800-122328200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr12:122327800-122328200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:122327800-122328200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr12:122327800-122328200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:122327800-122328200	Enhancers	Brain Substantia Nigra	brain
46	chr12:122327800-122328200	Enhancers	Fetal Brain Male	brain
47	chr12:122327800-122328200	Enhancers	Fetal Heart	heart
48	chr12:122327800-122328200	Enhancers	Fetal Lung	lung
49	chr12:122327800-122328200	Enhancers	Fetal Stomach	stomach
50	chr12:122327800-122328200	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links