Variant report

Variant	rs17109778
Chromosome Location	chr14:80170573-80170574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10483933	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11848654	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17109739	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes]
rs17109747	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17109760	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs17109764	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs17109772	1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17109775	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160920	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61993166	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61995221	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61995222	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61995223	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61995224	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61995225	0.91[AMR][1000 genomes];1.00[ASN][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	nsv1045241	chr14:79885361-80734201	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1039622	chr14:79908702-80266601	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17109778	CYB5R2	trans	brain	seeQTL
rs17109778	ADAMTS4	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:80161600-80175800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr14:80166600-80171200	Weak transcription	Fetal Kidney	kidney
3	chr14:80169000-80172000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:80169200-80175200	Weak transcription	Brain Substantia Nigra	brain
5	chr14:80169800-80173600	Enhancers	Fetal Intestine Large	intestine
6	chr14:80170000-80173400	Enhancers	Fetal Intestine Small	intestine
7	chr14:80170200-80172400	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr14:80170400-80171000	Enhancers	Colon Smooth Muscle	Colon
9	chr14:80170400-80173200	Enhancers	Fetal Lung	lung

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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