Variant report

Variant	rs2196489
Chromosome Location	chr12:29582144-29582145
allele	G/T
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:13)

rs_ID	r²[population]
rs10492379	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10492380	0.85[EUR][1000 genomes]
rs10843421	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11050241	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11613143	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12812922	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12823082	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12828155	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369900	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1369904	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1436315	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1436316	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs880133	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv898952	chr12:29565537-29617550	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv525100	chr12:29576517-29585955	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29571000-29583400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:29578000-29583200	Enhancers	Hela-S3	cervix
3	chr12:29579800-29583800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:29580000-29583400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:29580800-29582200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:29581200-29582400	Enhancers	HMEC	breast
7	chr12:29581200-29583800	Enhancers	Duodenum Mucosa	Duodenum
8	chr12:29581400-29582400	Enhancers	NHEK	skin
9	chr12:29581400-29582600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:29581400-29584000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:29581600-29583200	Weak transcription	K562	blood
12	chr12:29581600-29604200	Weak transcription	HSMMtube	muscle
13	chr12:29581800-29583000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:29581800-29613600	Weak transcription	Muscle Satellite Cultured Cells	--

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

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