Variant report

Variant	rs1444639
Chromosome Location	chr12:20549164-20549165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10841504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841505	0.97[ASN][1000 genomes]
rs10841508	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11045209	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs11045210	0.87[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs12299821	0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs1899908	1.00[CHB][hapmap];0.98[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	esv3435620	chr12:20547685-20549733	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
7	esv3420073	chr12:20548085-20549283	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1444639	PDE3A	cis	parietal	SCAN
rs1444639	LST-3TM12	cis	parietal	SCAN
rs1444639	SAA2	trans	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20538200-20550400	Weak transcription	HUVEC	blood vessel
2	chr12:20538200-20558000	Weak transcription	Left Ventricle	heart
3	chr12:20542600-20566200	Weak transcription	Aorta	Aorta
4	chr12:20543000-20549200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:20543000-20551000	Weak transcription	A549	lung
6	chr12:20544000-20556000	Weak transcription	Osteobl	bone
7	chr12:20544800-20555800	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:20546000-20549200	Weak transcription	Right Ventricle	heart
9	chr12:20548000-20549200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:20548200-20550800	Weak transcription	Hela-S3	cervix
11	chr12:20548200-20556000	Weak transcription	Fetal Intestine Large	intestine
12	chr12:20549000-20549200	Enhancers	Fetal Heart	heart
13	chr12:20549000-20549400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr12:20549000-20553200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:20549000-20555000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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