Variant report

Variant	rs12299821
Chromosome Location	chr12:20554993-20554994
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10743371	0.85[ASN][1000 genomes]
rs10841503	0.85[ASN][1000 genomes]
rs10841504	0.81[AMR][1000 genomes]
rs10841505	0.84[EUR][1000 genomes]
rs10841508	0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11045205	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11045209	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs11045210	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1444639	0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs1899908	0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv1042315	chr12:20531641-20629866	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12299821	LST-3TM12	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20538200-20558000	Weak transcription	Left Ventricle	heart
2	chr12:20542600-20566200	Weak transcription	Aorta	Aorta
3	chr12:20544000-20556000	Weak transcription	Osteobl	bone
4	chr12:20544800-20555800	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:20548200-20556000	Weak transcription	Fetal Intestine Large	intestine
6	chr12:20549000-20555000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:20549400-20555600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:20549400-20557800	Weak transcription	Right Ventricle	heart
9	chr12:20550400-20568200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:20551600-20556200	Weak transcription	HUVEC	blood vessel
11	chr12:20552000-20555800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:20552400-20555600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:20553000-20555800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:20553200-20555600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:20553200-20556000	Weak transcription	Fetal Heart	heart
16	chr12:20553200-20571200	Weak transcription	Psoas Muscle	Psoas
17	chr12:20554000-20557400	Genic enhancers	Hela-S3	cervix
18	chr12:20554200-20555600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:20554400-20555800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:20554800-20555400	Strong transcription	Fetal Intestine Small	intestine
21	chr12:20554800-20555800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:20554800-20556000	Weak transcription	H1 Cell Line	embryonic stem cell

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