Variant report

Variant	rs397311
Chromosome Location	chr6:145806701-145806702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1045820	0.85[CEU][hapmap]
rs10872579	0.84[CEU][hapmap]
rs11155438	0.82[CEU][hapmap]
rs12663211	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1292333	0.85[CEU][hapmap]
rs1292334	0.85[CEU][hapmap]
rs1292335	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs1292336	0.85[CEU][hapmap]
rs1292337	0.85[CEU][hapmap]
rs1355146	0.90[EUR][1000 genomes]
rs1396648	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1509213	0.81[EUR][1000 genomes]
rs1509214	0.80[EUR][1000 genomes]
rs1883406	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1883407	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1912023	0.80[EUR][1000 genomes]
rs1935617	0.81[EUR][1000 genomes]
rs365515	0.91[EUR][1000 genomes]
rs367612	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs371186	0.80[EUR][1000 genomes]
rs372378	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs373527	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs373704	0.83[EUR][1000 genomes]
rs373778	0.83[EUR][1000 genomes]
rs374464	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs375873	0.85[EUR][1000 genomes]
rs376991	0.81[ASN][1000 genomes]
rs377143	0.85[EUR][1000 genomes]
rs378937	0.82[EUR][1000 genomes]
rs380883	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs384453	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs386678	0.83[EUR][1000 genomes]
rs387376	0.80[EUR][1000 genomes]
rs388728	0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs391524	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs391820	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs392014	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395948	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs396492	0.85[EUR][1000 genomes]
rs398408	0.81[EUR][1000 genomes]
rs399516	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs400968	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs401888	0.81[ASN][1000 genomes]
rs404229	0.83[EUR][1000 genomes]
rs405622	0.81[EUR][1000 genomes]
rs406799	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs409553	0.80[EUR][1000 genomes]
rs411468	0.81[ASN][1000 genomes]
rs411641	0.81[ASN][1000 genomes]
rs413880	0.91[EUR][1000 genomes]
rs413916	0.81[ASN][1000 genomes]
rs414646	0.81[ASN][1000 genomes]
rs418662	0.85[EUR][1000 genomes]
rs419847	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs419850	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs421032	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs425999	0.80[EUR][1000 genomes]
rs428659	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs429306	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs430003	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs430561	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs436066	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4383831	0.82[EUR][1000 genomes]
rs439017	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439035	0.80[EUR][1000 genomes]
rs441290	0.80[EUR][1000 genomes]
rs441364	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs441477	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs442435	0.85[EUR][1000 genomes]
rs444564	0.84[EUR][1000 genomes]
rs446031	0.80[EUR][1000 genomes]
rs450076	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs450973	0.83[EUR][1000 genomes]
rs451349	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs452552	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs453609	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs453834	0.80[EUR][1000 genomes]
rs454614	0.81[ASN][1000 genomes]
rs455109	0.83[EUR][1000 genomes]
rs4896820	0.80[EUR][1000 genomes]
rs4896832	0.85[CEU][hapmap]
rs4896833	0.85[CEU][hapmap]
rs621382	0.81[EUR][1000 genomes]
rs6570701	0.85[CEU][hapmap]
rs6570703	0.90[CEU][hapmap]
rs6570705	0.85[CEU][hapmap]
rs6570708	0.82[CEU][hapmap]
rs6899900	0.80[EUR][1000 genomes]
rs6918814	0.82[EUR][1000 genomes]
rs6919684	0.80[EUR][1000 genomes]
rs6941429	0.82[CEU][hapmap]
rs697053	0.82[CEU][hapmap]
rs697054	0.82[CEU][hapmap]
rs697055	0.82[CEU][hapmap]
rs702304	0.82[CEU][hapmap]
rs702306	0.80[CEU][hapmap]
rs702307	0.82[CEU][hapmap]
rs702318	0.82[CEU][hapmap]
rs857875	0.85[CEU][hapmap]
rs857877	0.85[CEU][hapmap]
rs857879	0.85[CEU][hapmap]
rs857880	0.85[CEU][hapmap]
rs857881	0.81[CEU][hapmap]
rs857882	0.85[CEU][hapmap]
rs857883	0.85[CEU][hapmap]
rs9376955	0.81[CEU][hapmap]
rs9376956	0.85[CEU][hapmap]
rs9390326	0.91[EUR][1000 genomes]
rs9390327	0.89[EUR][1000 genomes]
rs9390329	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9399549	0.91[EUR][1000 genomes]
rs9399555	0.80[EUR][1000 genomes]
rs9399561	0.82[CEU][hapmap]
rs9403706	0.91[EUR][1000 genomes]
rs9403707	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9403737	0.85[CEU][hapmap]
rs9484995	0.89[EUR][1000 genomes]
rs9497316	0.89[EUR][1000 genomes]
rs9497380	0.85[CEU][hapmap]
rs973855	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs973856	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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	nsv1017166	chr6:145677071-145808448	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv604838	chr6:145709371-145841146	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv520619	chr6:145800915-145807907	Enhancers Active TSS Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
4	esv2763962	chr6:145802158-145817051	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs397311	SHPRH	cis	cerebellum	SCAN
rs397311	SHPRH	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145806400-145806800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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