Variant report

Variant	rs17499670
Chromosome Location	chr7:38489731-38489732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10951558	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12154302	0.91[EUR][1000 genomes]
rs12673437	0.90[GIH][hapmap]
rs1558617	0.91[EUR][1000 genomes]
rs17171359	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs17171367	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs17171377	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs17171384	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs17498899	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17506922	0.81[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1861239	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs34057414	0.91[EUR][1000 genomes]
rs3735089	0.90[GIH][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs3778879	0.90[EUR][1000 genomes]
rs3778882	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs3823591	0.90[GIH][hapmap];0.80[MKK][hapmap]
rs3823594	0.88[MKK][hapmap];0.83[TSI][hapmap]
rs41279585	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv1020990	chr7:38257707-38503472	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv1031936	chr7:38319437-38503472	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv830965	chr7:38350614-38521047	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv830966	chr7:38393663-38602553	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv887964	chr7:38457144-38501065	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1825425	chr7:38457144-38507180	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1815666	chr7:38485901-38499850	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17499670	AMPH	cis	Adipose Subcutaneous	GTEx
rs17499670	AMPH	cis	normal skin	skin_eQTL
rs17499670	AMPH	cis	Nerve Tibial	GTEx
rs17499670	AMPH	cis	Skin Sun Exposed Lower leg	GTEx
rs17499670	AMPH	cis	Muscle Skeletal	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38467800-38495600	Weak transcription	Aorta	Aorta
2	chr7:38468400-38492000	Weak transcription	Fetal Heart	heart
3	chr7:38469200-38491600	Weak transcription	Fetal Stomach	stomach
4	chr7:38471200-38492200	Weak transcription	Fetal Lung	lung
5	chr7:38471800-38498200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:38476000-38501600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:38487600-38489800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:38488600-38489800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:38489000-38489800	Enhancers	Brain Angular Gyrus	brain
10	chr7:38489000-38491600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:38489600-38489800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:38489600-38489800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	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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