Variant report

Variant	rs1682579
Chromosome Location	chr12:83384334-83384335
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10746262	0.90[EUR][1000 genomes]
rs10778918	0.88[EUR][1000 genomes]
rs10778921	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1434425	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1655611	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1655612	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1682567	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1682575	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1682580	0.94[EUR][1000 genomes]
rs1682606	0.90[EUR][1000 genomes]
rs1682608	0.90[EUR][1000 genomes]
rs1796150	0.86[EUR][1000 genomes]
rs1796157	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1796161	0.90[EUR][1000 genomes]
rs1796162	0.90[EUR][1000 genomes]
rs1796166	0.86[EUR][1000 genomes]
rs1796167	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1796168	0.90[EUR][1000 genomes]
rs1796178	0.86[EUR][1000 genomes]
rs1796187	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1796296	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1796300	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1821444	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1972801	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2019434	0.84[AMR][1000 genomes]
rs2046417	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2062357	0.90[EUR][1000 genomes]
rs2403025	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2403026	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2707753	0.90[EUR][1000 genomes]
rs2707754	0.90[EUR][1000 genomes]
rs2707760	0.84[EUR][1000 genomes]
rs2708000	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4882531	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539697	0.98[EUR][1000 genomes]
rs7297707	0.84[EUR][1000 genomes]
rs7299175	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7303058	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7953974	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	nsv1047239	chr12:83362299-83444855	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83357800-83389600	Weak transcription	Fetal Intestine Large	intestine
2	chr12:83358000-83389600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:83358400-83397600	Weak transcription	Brain Anterior Caudate	brain
4	chr12:83358400-83409200	Weak transcription	Brain Angular Gyrus	brain
5	chr12:83358600-83394200	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:83358600-83399600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:83358600-83409400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:83367400-83391800	Weak transcription	Small Intestine	intestine
9	chr12:83368800-83386800	Weak transcription	Fetal Stomach	stomach
10	chr12:83368800-83393800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:83368800-83399200	Weak transcription	Esophagus	oesophagus
12	chr12:83374600-83390000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:83375600-83405600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:83377600-83400000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:83377600-83409400	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:83377800-83410200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:83378000-83384400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:83378000-83389200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:83378200-83391800	Weak transcription	Fetal Heart	heart
20	chr12:83378400-83394200	Weak transcription	Lung	lung
21	chr12:83378400-83409600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:83378600-83389600	Weak transcription	Pancreas	Pancrea
23	chr12:83378800-83409000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:83379000-83389800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr12:83379200-83397000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:83379600-83386600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:83379800-83393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:83380000-83394200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:83380000-83403200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:83380000-83409200	Weak transcription	Gastric	stomach
31	chr12:83380200-83397200	Weak transcription	Brain Substantia Nigra	brain
32	chr12:83380600-83385200	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:83381800-83399400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:83382000-83385000	Weak transcription	Brain Germinal Matrix	brain
35	chr12:83382000-83388200	Weak transcription	Fetal Intestine Small	intestine
36	chr12:83382000-83393000	Weak transcription	Fetal Lung	lung
37	chr12:83382400-83384400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:83382400-83399000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:83382600-83399200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:83382800-83388200	Weak transcription	Fetal Kidney	kidney
41	chr12:83383600-83384400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:83384000-83397000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:83384200-83386200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links