Variant report

Variant	rs892539
Chromosome Location	chr12:83379424-83379425
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1023967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1025556	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1032122	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10506881	0.82[TSI][hapmap]
rs10778923	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10862531	0.81[TSI][hapmap]
rs10862533	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318295	1.00[ASN][1000 genomes]
rs12816354	1.00[ASN][1000 genomes]
rs12821905	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1796156	1.00[CHB][hapmap]
rs2019662	0.81[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2403024	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3993375	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7296753	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7300355	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7308937	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7960659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83347000-83379600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:83356400-83381600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:83356600-83381400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:83357800-83389600	Weak transcription	Fetal Intestine Large	intestine
5	chr12:83358000-83389600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:83358400-83397600	Weak transcription	Brain Anterior Caudate	brain
7	chr12:83358400-83409200	Weak transcription	Brain Angular Gyrus	brain
8	chr12:83358600-83394200	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:83358600-83399600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:83358600-83409400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:83362000-83382200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:83364200-83379600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:83367400-83391800	Weak transcription	Small Intestine	intestine
14	chr12:83368800-83379600	Weak transcription	Fetal Lung	lung
15	chr12:83368800-83386800	Weak transcription	Fetal Stomach	stomach
16	chr12:83368800-83393800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:83368800-83399200	Weak transcription	Esophagus	oesophagus
18	chr12:83371600-83379600	Weak transcription	Gastric	stomach
19	chr12:83374600-83390000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:83375400-83379600	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:83375600-83405600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:83376000-83381200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:83377600-83400000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:83377600-83409400	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:83377800-83410200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:83378000-83384400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:83378000-83389200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:83378200-83382400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:83378200-83391800	Weak transcription	Fetal Heart	heart
30	chr12:83378400-83394200	Weak transcription	Lung	lung
31	chr12:83378400-83409600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:83378600-83389600	Weak transcription	Pancreas	Pancrea
33	chr12:83378800-83409000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:83379000-83382400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:83379000-83389800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:83379200-83397000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:83379400-83379800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:83379400-83380000	Strong transcription	Brain Cingulate Gyrus	brain
39	chr12:83379400-83380000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:83379400-83380200	Strong transcription	Brain Substantia Nigra	brain
41	chr12:83379400-83382000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:83379400-83383600	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links