Variant report

Variant	rs4845317
Chromosome Location	chr1:152670341-152670342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:152670228-152670578	HUVEC	blood vessel:	n/a	chr1:152670404-152670416

Variant related genes	Relation type
LCE2A	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1011297	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10749673	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788843	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788844	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10888504	0.94[CHD][hapmap]
rs10888505	0.94[CHD][hapmap]
rs10888506	0.84[ASN][1000 genomes]
rs10888507	0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs11205045	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205046	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205047	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205048	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205049	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205050	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205060	0.94[CHD][hapmap]
rs11205061	0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs11205062	0.85[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs11205066	0.85[CHB][hapmap]
rs11205072	0.86[ASN][1000 genomes]
rs11205073	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11205078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205083	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs11580546	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11581621	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11582021	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11587218	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032251	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12041270	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12043198	0.86[ASN][1000 genomes]
rs12071335	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12074783	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs12081753	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12081793	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12239432	0.83[ASN][1000 genomes]
rs12239456	0.83[ASN][1000 genomes]
rs12564254	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564476	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12566080	0.83[ASN][1000 genomes]
rs12728742	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12745646	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12752346	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1325508	0.83[ASN][1000 genomes]
rs1332497	0.84[CHB][hapmap];0.92[CHD][hapmap]
rs1359515	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1359516	0.83[ASN][1000 genomes]
rs1412542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1474168	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474169	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1575753	0.83[ASN][1000 genomes]
rs1581802	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1581804	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1819470	0.85[CHB][hapmap]
rs1853805	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1886732	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs1888966	0.86[ASN][1000 genomes]
rs1925661	0.85[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs1925663	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1930126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753453	0.85[CHB][hapmap]
rs3904413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3904414	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs3904415	0.87[ASN][1000 genomes]
rs3908717	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs4287181	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4320779	0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs4353096	0.83[ASN][1000 genomes]
rs4540662	0.83[ASN][1000 genomes]
rs4845456	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845457	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs512208	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55644922	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55687384	0.83[ASN][1000 genomes]
rs59349974	0.82[ASN][1000 genomes]
rs59540569	0.83[ASN][1000 genomes]
rs59633986	0.83[ASN][1000 genomes]
rs59863780	0.85[ASN][1000 genomes]
rs60208884	0.83[ASN][1000 genomes]
rs60350222	0.83[ASN][1000 genomes]
rs60861680	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61813877	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6660162	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6662989	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671975	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6687570	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6687574	1.00[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs6687682	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6702474	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73009167	0.86[ASN][1000 genomes]
rs7527788	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7540520	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs908929	0.94[CHD][hapmap]
rs925976	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs925977	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942826	0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs942827	0.83[ASN][1000 genomes]
rs960752	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]
rs989831	0.83[ASN][1000 genomes]
rs989832	0.83[ASN][1000 genomes]
rs989833	0.83[ASN][1000 genomes]
rs989834	0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs9970033	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9970657	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
12	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
13	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
14	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv3692902	chr1:152669367-152732567	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv947325	chr1:152670204-152793272	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4845317	PMVK	cis	cerebellum	SCAN
rs4845317	SMCP	cis	cerebellum	SCAN
rs4845317	NUP210L	cis	parietal	SCAN
rs4845317	LOR	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152669000-152670400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:152670200-152670600	Enhancers	HMEC	breast
3	chr1:152670200-152672200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:152670200-152672400	Enhancers	NHLF	lung

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