Variant report

Variant	rs235997
Chromosome Location	chr16:71284193-71284194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10775325	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs109556	0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs11865544	0.85[CEU][hapmap]
rs171013	0.82[EUR][1000 genomes]
rs235996	0.81[EUR][1000 genomes]
rs236006	0.84[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs236012	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3094450	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3096375	0.81[JPT][hapmap]
rs3096381	0.82[GIH][hapmap]
rs4570853	0.85[CEU][hapmap]
rs9889153	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9938525	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758429	chr16:70807122-71316983	Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv2758653	chr16:70807122-71316983	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv482374	chr16:71228600-71401617	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1860	chr16:71269156-71313852	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs235997	HYDIN	cis	parietal	SCAN
rs235997	TERF2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71279400-71289000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:71279600-71288800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:71279800-71284200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:71283200-71285000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr16:71283400-71284800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr16:71283400-71285200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr16:71283600-71288800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr16:71283800-71288800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr16:71283800-71289000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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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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