Variant report

Variant	rs1899909
Chromosome Location	chr12:20544707-20544708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10743371	0.86[EUR][1000 genomes]
rs10770645	0.85[CEU][hapmap]
rs10770647	0.84[EUR][1000 genomes]
rs10770648	0.86[EUR][1000 genomes]
rs10841506	0.92[CEU][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11045219	0.90[EUR][1000 genomes]
rs1348582	0.80[EUR][1000 genomes]
rs1530446	0.85[CEU][hapmap]
rs61246087	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61911356	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61911357	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]

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

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20533200-20544800	Weak transcription	Right Atrium	heart
2	chr12:20538200-20550400	Weak transcription	HUVEC	blood vessel
3	chr12:20538200-20558000	Weak transcription	Left Ventricle	heart
4	chr12:20540600-20546200	Enhancers	Fetal Intestine Large	intestine
5	chr12:20542400-20545600	Weak transcription	Right Ventricle	heart
6	chr12:20542600-20566200	Weak transcription	Aorta	Aorta
7	chr12:20543000-20547000	Weak transcription	Small Intestine	intestine
8	chr12:20543000-20549200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:20543000-20551000	Weak transcription	A549	lung
10	chr12:20544000-20546600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:20544000-20546800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:20544000-20547800	Weak transcription	Fetal Heart	heart
13	chr12:20544000-20556000	Weak transcription	Osteobl	bone
14	chr12:20544400-20545600	Enhancers	Fetal Intestine Small	intestine
15	chr12:20544600-20544800	Enhancers	Colonic Mucosa	Colon
16	chr12:20544600-20544800	Enhancers	Colon Smooth Muscle	Colon
17	chr12:20544600-20544800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr12:20544600-20545000	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr12:20544600-20545400	Strong transcription	Hela-S3	cervix

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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