Variant report

Variant	rs12097690
Chromosome Location	chr1:77461668-77461669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11162237	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11162238	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11162239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11162240	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11162241	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11162242	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12092330	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58321490	1.00[AMR][1000 genomes]
rs6670588	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73001579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73003391	1.00[AMR][1000 genomes]
rs73005304	1.00[AMR][1000 genomes]
rs73005305	1.00[AMR][1000 genomes]
rs73005309	1.00[AMR][1000 genomes]
rs73005320	1.00[AMR][1000 genomes]
rs73005325	1.00[AMR][1000 genomes]
rs73005327	1.00[AMR][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	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv830292	chr1:77425571-77584307	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77456800-77472400	Weak transcription	Aorta	Aorta
2	chr1:77459400-77464000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:77459600-77463400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:77459600-77463400	Weak transcription	NHDF-Ad	bronchial
5	chr1:77459600-77463800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:77460400-77476200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:77460600-77462000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:77461000-77461800	Active TSS	NHEK	skin
9	chr1:77461000-77462000	Active TSS	HMEC	breast
10	chr1:77461000-77462200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:77461000-77462200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:77461600-77462000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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