Variant report

Variant	rs11829960
Chromosome Location	chr12:83453467-83453468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10506888	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11115559	0.81[EUR][1000 genomes]
rs11832231	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832789	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11834840	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12315590	0.82[EUR][1000 genomes]
rs17010538	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17010563	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17010565	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17010567	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17010576	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010577	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17010578	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17010580	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17010586	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033576	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304787	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83419000-83468000	Weak transcription	Fetal Stomach	stomach
2	chr12:83436800-83467800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:83437200-83454400	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:83437200-83467800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:83438600-83462400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:83443400-83460400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:83443400-83476400	Weak transcription	Fetal Lung	lung
8	chr12:83445600-83454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:83446000-83457800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:83446600-83456600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:83447200-83454600	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:83449400-83454800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:83450800-83462400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:83451400-83454200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:83451800-83454600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:83453000-83454200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:83453000-83455600	Weak transcription	Monocytes-CD14+_RO01746	blood

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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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