Variant report

Variant	rs12402969
Chromosome Location	chr1:160020237-160020238
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:11)

rs_ID	r²[population]
rs11265317	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11265328	0.83[AFR][1000 genomes]
rs1131891	0.82[CEU][hapmap]
rs1186675	0.84[AMR][1000 genomes]
rs12408584	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17846705	0.83[AFR][1000 genomes]
rs56211999	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs56282521	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61822013	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs61822015	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs970365	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160002600-160022800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:160015000-160032400	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr1:160015400-160031600	Enhancers	Brain Angular Gyrus	brain
4	chr1:160016400-160025400	Enhancers	Brain Substantia Nigra	brain
5	chr1:160016600-160031000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:160016600-160039800	Weak transcription	Right Atrium	heart
7	chr1:160017000-160031600	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:160017200-160025600	Enhancers	Brain Anterior Caudate	brain
9	chr1:160017400-160023400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:160017800-160023800	Enhancers	Brain Hippocampus Middle	brain
11	chr1:160019200-160031200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:160019200-160036400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:160019600-160020600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:160019600-160021600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:160020000-160022600	Enhancers	HepG2	liver
16	chr1:160020200-160025600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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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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