Variant report

Variant	rs9816597
Chromosome Location	chr3:139265966-139265967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10935331	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs167188	0.89[EUR][1000 genomes]
rs16849083	0.82[LWK][hapmap]
rs176990	1.00[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs190910	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2071387	0.81[CHB][hapmap]
rs211586	0.96[EUR][1000 genomes]
rs295491	0.82[LWK][hapmap]
rs295495	0.89[LWK][hapmap]
rs295497	0.92[ASN][1000 genomes]
rs295498	0.95[ASN][1000 genomes]
rs295501	0.86[EUR][1000 genomes]
rs3772881	0.94[ASW][hapmap]
rs4564921	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6797111	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs893704	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9825927	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826668	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9816597	MRPS22	cis	parietal	SCAN
rs9816597	TRPC1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139259200-139307000	Weak transcription	Aorta	Aorta
2	chr3:139261200-139279400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:139265000-139266000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:139265200-139266000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:139265600-139266000	Enhancers	Lung	lung
6	chr3:139265600-139266200	Genic enhancers	Fetal Stomach	stomach
7	chr3:139265600-139266400	Strong transcription	Fetal Intestine Small	intestine
8	chr3:139265600-139269000	Enhancers	Pancreas	Pancrea
9	chr3:139265600-139269400	Enhancers	Ovary	ovary
10	chr3:139265800-139274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:139265800-139290600	Weak transcription	Adipose Nuclei	Adipose

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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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