Variant report

Variant	rs808943
Chromosome Location	chr20:16016157-16016158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10485544	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs6034354	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6034355	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs6043677	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs6043678	0.86[EUR][1000 genomes]
rs6043680	0.83[CEU][hapmap]
rs6043681	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6043682	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs6043683	0.83[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs6080102	0.96[YRI][hapmap]
rs6135652	0.96[YRI][hapmap]
rs73241683	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs775132	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs775134	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs775135	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775138	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3447866	chr20:15799286-16115291	Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1065548	chr20:15971797-16023086	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1059778	chr20:15999519-16165895	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv544207	chr20:15999519-16165895	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv585649	chr20:16004320-16066764	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1061301	chr20:16007489-16097070	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1061171	chr20:16011943-16024267	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs808943	SEC23B	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16009000-16017200	Weak transcription	Fetal Brain Male	brain
2	chr20:16011200-16016600	Weak transcription	Primary B cells from cord blood	blood
3	chr20:16011400-16017200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr20:16016000-16016200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr20:16016000-16016400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr20:16016000-16016600	Enhancers	ES-I3 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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