Variant report

Variant	rs960752
Chromosome Location	chr1:152597371-152597372
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1011297	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749673	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10788843	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10788844	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888504	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs10888505	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs10888506	0.86[ASN][1000 genomes]
rs10888507	0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs11205045	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205046	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205047	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205048	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205049	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205050	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205060	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs11205061	0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs11205062	0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs11205072	0.85[ASN][1000 genomes]
rs11205073	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11205078	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205080	0.89[ASW][hapmap];0.94[YRI][hapmap]
rs11205083	0.89[JPT][hapmap]
rs11205084	0.81[ASW][hapmap];0.88[YRI][hapmap]
rs11580546	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581621	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582021	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587218	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032251	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041270	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043198	0.85[ASN][1000 genomes]
rs12071335	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12074783	0.83[ASN][1000 genomes]
rs12081753	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081793	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239432	0.87[ASN][1000 genomes]
rs12239456	0.87[ASN][1000 genomes]
rs12564254	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564476	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12566080	0.87[ASN][1000 genomes]
rs12728742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745646	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752346	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325508	0.87[ASN][1000 genomes]
rs1332497	0.94[CHD][hapmap]
rs1359515	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359516	0.87[ASN][1000 genomes]
rs1412542	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1474168	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474169	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1575753	0.87[ASN][1000 genomes]
rs1581802	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581804	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1853805	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1886732	0.85[ASN][1000 genomes]
rs1888966	0.85[ASN][1000 genomes]
rs1925661	0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs1925663	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1930126	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2224986	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs3904413	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3904414	0.82[ASN][1000 genomes]
rs3904415	0.83[ASN][1000 genomes]
rs3908717	0.83[ASN][1000 genomes]
rs4287181	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4320779	0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs4353096	0.87[ASN][1000 genomes]
rs4540662	0.87[ASN][1000 genomes]
rs4845317	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845445	0.85[EUR][1000 genomes]
rs4845456	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845457	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512208	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55644922	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55687384	0.87[ASN][1000 genomes]
rs59349974	0.84[ASN][1000 genomes]
rs59540569	0.87[ASN][1000 genomes]
rs59633986	0.87[ASN][1000 genomes]
rs59863780	0.87[ASN][1000 genomes]
rs60208884	0.87[ASN][1000 genomes]
rs60350222	0.87[ASN][1000 genomes]
rs60861680	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61813877	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6660162	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662989	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671975	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687570	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687574	0.89[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs6687682	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73009167	0.85[ASN][1000 genomes]
rs7527788	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540520	0.86[EUR][1000 genomes]
rs908929	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs925976	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925977	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942826	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs942827	0.87[ASN][1000 genomes]
rs989831	0.87[ASN][1000 genomes]
rs989832	0.87[ASN][1000 genomes]
rs989833	0.87[ASN][1000 genomes]
rs989834	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs9970033	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970657	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2750810	chr1:152453669-152660927	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1827111	chr1:152472839-152690073	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv1830764	chr1:152472839-152690073	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv547878	chr1:152530510-152597948	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv2888	chr1:152532137-152620444	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv68	chr1:152549956-152608472	Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv33483	chr1:152550269-152775526	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv872447	chr1:152551276-152643160	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv535168	chr1:152555074-152617494	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2764248	chr1:152555527-152597371	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv547891	chr1:152556085-152770446	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv872448	chr1:152561408-152643160	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv469873	chr1:152563260-152713616	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv482518	chr1:152563260-152713616	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv535169	chr1:152572876-152600388	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv1001647	chr1:152572876-152678509	Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
20	nsv872449	chr1:152583678-152643160	Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs960752	SMCP	cis	cerebellum	SCAN
rs960752	VPS45	cis	cerebellum	SCAN
rs960752	RPTN	cis	cerebellum	SCAN
rs960752	NUP210L	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152596400-152599400	Weak transcription	Adipose Nuclei	Adipose
2	chr1:152597000-152599200	Weak transcription	HSMM	muscle

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