Variant report

Variant	rs12409512
Chromosome Location	chr1:210794975-210794976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12406888	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12409881	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12732352	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs12735867	0.85[CEU][hapmap]
rs12739187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12754319	0.85[CEU][hapmap]
rs34258739	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827410	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827412	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61827413	0.87[AMR][1000 genomes];0.94[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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv522480	chr1:210779936-210848344	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
3	esv1825229	chr1:210789477-210854976	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210790400-210801800	Weak transcription	Pancreas	Pancrea
2	chr1:210790600-210796800	Weak transcription	Ovary	ovary
3	chr1:210790600-210807000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:210790800-210795000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:210792800-210795200	Enhancers	Brain Hippocampus Middle	brain
6	chr1:210793000-210795000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:210793400-210795800	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:210793600-210795400	Enhancers	Brain Angular Gyrus	brain
9	chr1:210793600-210795800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr1:210793800-210795200	Enhancers	Brain Anterior Caudate	brain
11	chr1:210793800-210797800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:210794000-210795200	Weak transcription	HSMMtube	muscle
13	chr1:210794600-210795200	Enhancers	Brain Germinal Matrix	brain
14	chr1:210794600-210795200	Weak transcription	Brain Substantia Nigra	brain
15	chr1:210794800-210796200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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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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