Variant report

Variant	rs4405126
Chromosome Location	chr1:196067431-196067432
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10801516	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12031315	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038314	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12040221	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12041004	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12041804	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12562741	0.82[EUR][1000 genomes]
rs12567147	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16839499	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16839508	0.92[EUR][1000 genomes]
rs4436369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4614237	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59310826	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61471621	0.89[EUR][1000 genomes]
rs61822088	0.89[EUR][1000 genomes]
rs7520705	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538355	0.90[EUR][1000 genomes]
rs7543048	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757765	chr1:195803764-196119454	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2758989	chr1:195803764-196119454	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv872948	chr1:195872295-196236425	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv470769	chr1:195901676-196187665	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv467339	chr1:195912579-196119310	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv548738	chr1:195912579-196119310	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv534209	chr1:196011881-196208885	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv872951	chr1:196027872-196166278	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr1:196065600-196067600	Enhancers	Fetal Lung	lung
2	chr1:196066000-196067600	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr1:196066200-196068200	Enhancers	Brain Cingulate Gyrus	brain
4	chr1:196066400-196067600	Enhancers	Brain Substantia Nigra	brain
5	chr1:196066400-196067800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:196066600-196067600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:196066600-196067600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:196066600-196067800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:196066800-196067800	Enhancers	Brain Anterior Caudate	brain
10	chr1:196067000-196067600	Weak transcription	Brain Germinal Matrix	brain
11	chr1:196067000-196067800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:196067400-196069200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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