Variant report

Variant	rs16908019
Chromosome Location	chr12:12558145-12558146
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12557174..12559424-chr12:12713133..12714808,2	MCF-7	breast:
2	chr12:12550932..12553792-chr12:12558043..12559658,2	K562	blood:
3	chr12:12550258..12553161-chr12:12554299..12558157,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11831188	1.00[ASN][1000 genomes]
rs11831555	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908006	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861674	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2193270	0.96[AFR][1000 genomes]
rs4763824	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763827	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763828	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4763831	0.83[ASN][1000 genomes]
rs56261569	0.81[ASN][1000 genomes]
rs58218344	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58529509	1.00[ASN][1000 genomes]
rs60022096	1.00[ASN][1000 genomes]
rs60363317	1.00[ASN][1000 genomes]
rs60971404	1.00[ASN][1000 genomes]
rs6488521	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488523	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6488524	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6488527	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7133988	1.00[ASN][1000 genomes]
rs7134787	1.00[ASN][1000 genomes]
rs714480	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306292	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73287587	1.00[ASN][1000 genomes]
rs7957014	1.00[ASN][1000 genomes]
rs7973069	1.00[ASN][1000 genomes]
rs7975061	1.00[ASN][1000 genomes]
rs7978842	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7980390	1.00[ASN][1000 genomes]
rs888198	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
4	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
7	chr12:12543000-12558800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:12551000-12559000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:12551200-12558800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:12551600-12558800	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:12552000-12558800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:12552000-12558800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:12552000-12558800	Weak transcription	Lung	lung
14	chr12:12552000-12559000	Weak transcription	HSMM	muscle
15	chr12:12552000-12559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:12552000-12561400	Weak transcription	HSMMtube	muscle
17	chr12:12552000-12569000	Weak transcription	Hela-S3	cervix
18	chr12:12552200-12558600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:12552800-12558600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:12552800-12558800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:12553200-12561400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:12553400-12558400	Weak transcription	Brain Anterior Caudate	brain
23	chr12:12553400-12558600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:12553400-12558800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:12553400-12558800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:12553400-12559000	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:12554200-12558600	Weak transcription	GM12878-XiMat	blood
28	chr12:12555000-12560600	Enhancers	Fetal Intestine Large	intestine
29	chr12:12555200-12559200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr12:12555200-12560200	Enhancers	Fetal Intestine Small	intestine
31	chr12:12555200-12560800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr12:12555400-12559200	Enhancers	Placenta	Placenta
33	chr12:12555600-12558600	Weak transcription	Aorta	Aorta
34	chr12:12556000-12559000	Enhancers	Brain Substantia Nigra	brain
35	chr12:12556000-12560000	Enhancers	Liver	Liver
36	chr12:12556000-12560200	Enhancers	Stomach Mucosa	stomach
37	chr12:12556200-12558800	Enhancers	Brain Hippocampus Middle	brain
38	chr12:12556200-12560200	Enhancers	Brain Cingulate Gyrus	brain
39	chr12:12556200-12560200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr12:12556400-12558200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr12:12556600-12559800	Weak transcription	Left Ventricle	heart
42	chr12:12556600-12561600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:12556800-12559800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:12556800-12560200	Enhancers	HepG2	liver
45	chr12:12556800-12561000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:12556800-12561800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:12557000-12558400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:12557000-12558800	Weak transcription	Adipose Nuclei	Adipose
49	chr12:12557000-12558800	Weak transcription	Fetal Lung	lung
50	chr12:12557000-12559400	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links