Variant report

Variant	rs2764407
Chromosome Location	chr1:156333831-156333832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2246476	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs2253358	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[YRI][hapmap]
rs2495269	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2540168	0.95[CHB][hapmap];0.83[YRI][hapmap]
rs2540169	0.90[CHB][hapmap];0.88[YRI][hapmap]
rs2764406	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2985711	0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv915822	chr1:156226286-156651655	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases
4	nsv872471	chr1:156287360-156356480	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2764407	SMG5	cis	Whole Blood	GTEx
rs2764407	PAQR6	cis	Whole Blood	GTEx
rs2764407	C1orf85	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156327600-156336600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:156327600-156336600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:156330800-156335200	Weak transcription	Fetal Intestine Large	intestine
4	chr1:156330800-156335800	Weak transcription	Fetal Intestine Small	intestine
5	chr1:156331200-156334200	Weak transcription	HepG2	liver
6	chr1:156333600-156334400	Weak transcription	Pancreas	Pancrea

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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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