Variant report

Variant	rs1920664
Chromosome Location	chr3:160304614-160304615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160284666..160286841-chr3:160302799..160304775,2	MCF-7	breast:
2	chr3:160298872..160300468-chr3:160304100..160306105,2	K562	blood:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10212236	0.90[ASN][1000 genomes]
rs1047210	0.81[CEU][hapmap]
rs11706810	0.81[CEU][hapmap]
rs1317365	0.85[CEU][hapmap]
rs13403	0.83[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.83[ASN][1000 genomes]
rs1451761	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs1451762	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1451764	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1551190	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584688	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17236473	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs17236544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17570467	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17826221	0.81[CEU][hapmap]
rs1882126	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1882127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1920642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920662	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279457	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs2305407	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2366969	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28705750	0.93[ASN][1000 genomes]
rs2886825	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732706	0.82[CEU][hapmap]
rs3732707	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3773372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3851365	0.81[CEU][hapmap]
rs3851366	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs4091703	0.88[ASN][1000 genomes]
rs4292273	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4292274	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4621370	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679655	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679885	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[ASN][1000 genomes]
rs4679888	0.84[EUR][1000 genomes]
rs4679889	0.90[ASN][1000 genomes]
rs4679890	0.96[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679896	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4679899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679900	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680579	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs4680580	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs4680585	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs4680587	0.88[ASN][1000 genomes]
rs4680588	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs56197102	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58322641	0.90[ASN][1000 genomes]
rs60460891	0.85[ASN][1000 genomes]
rs62272791	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62272792	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62272794	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62272800	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62272810	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441319	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs6441320	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs6441324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768975	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793560	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6798668	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs6801300	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806505	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808083	0.82[CHB][hapmap]
rs721022	0.82[ASW][hapmap];0.84[CEU][hapmap]
rs721023	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7611130	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap]
rs7618974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7621724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627749	0.90[ASN][1000 genomes]
rs7627756	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7629	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[ASN][1000 genomes]
rs7629202	0.84[ASN][1000 genomes]
rs7629423	0.80[JPT][hapmap]
rs7631792	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap]
rs7634108	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7634826	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs7640072	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7643779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644453	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7645832	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7647873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9862595	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9968151	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription 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 miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv4089	chr3:160284848-160330024	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1920664	EGFL6	trans	lymphoblastoid	seeQTL
rs1920664	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs1920664	IFT80	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160299000-160305000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:160304000-160306000	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:160304600-160306000	Enhancers	Skeletal Muscle Male	skeletal muscle

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