Variant report

Variant	rs7618924
Chromosome Location	chr3:160855599-160855600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs10433352	0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs11712713	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11715733	0.84[AMR][1000 genomes]
rs11717272	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720263	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915989	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11922957	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11922959	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696112	0.80[AMR][1000 genomes]
rs12696113	0.80[AMR][1000 genomes]
rs13060601	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060718	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13061088	0.85[ASN][1000 genomes]
rs13071892	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13085336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13098896	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1374787	0.81[MEX][hapmap]
rs1382429	0.88[CHD][hapmap]
rs1562464	0.90[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs1599388	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831796	0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs16831886	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2014810	0.84[AMR][1000 genomes]
rs2044571	0.90[CEU][hapmap]
rs2889390	0.81[JPT][hapmap]
rs34105342	0.82[AMR][1000 genomes]
rs34221255	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34630898	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35127376	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35589595	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35914913	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4494975	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4521287	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4679929	0.81[AMR][1000 genomes]
rs4856700	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4856703	0.89[CHD][hapmap]
rs57145341	0.82[AMR][1000 genomes]
rs6441362	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6772723	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6794882	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806015	0.89[AMR][1000 genomes]
rs68166680	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73021215	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73023235	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610432	0.84[AMR][1000 genomes]
rs7624185	0.90[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7628389	0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs7638370	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs898677	0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs964533	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9812507	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9822435	0.90[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9832109	0.90[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9857855	0.84[AMR][1000 genomes]
rs9860537	0.90[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs9862086	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9876142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880269	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9883566	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv963285	chr3:160848780-160856433	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7618924	PPM1L	cis	cerebellum	SCAN
rs7618924	NMD3	cis	parietal	SCAN
rs7618924	B3GALNT1	cis	lymphoblastoid	seeQTL
rs7618924	B3GALT3	cis	multi-tissue	Pritchard
rs7618924	SPTSSB	cis	Adipose Subcutaneous	GTEx
rs7618924	SPTSSB	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160844600-160859000	Weak transcription	Left Ventricle	heart
2	chr3:160850400-160882400	Weak transcription	Ovary	ovary
3	chr3:160853800-160856000	Weak transcription	Lung	lung
4	chr3:160854800-160855800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:160855000-160855600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:160855000-160855800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:160855000-160855800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr3:160855200-160855600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:160855400-160855800	Enhancers	HUES64 Cell Line	embryonic stem cell

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