Variant report

Variant	rs4577423
Chromosome Location	chr3:155899665-155899666
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	STAT3	chr3:155899374-155899685	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:155899293-155899863	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr3:155899184-155899869	SK-N-SH	brain:	n/a	n/a
4	FOSL2	chr3:155899171-155899803	SK-N-SH	brain:	n/a	n/a
5	FOS	chr3:155899295-155899743	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr3:155899336-155899865	SK-N-SH	brain:	n/a	n/a
7	STAT3	chr3:155899305-155899676	MCF10A-Er-Src	breast:	n/a	n/a
8	PBX3	chr3:155899092-155899829	SK-N-SH	brain:	n/a	n/a
9	YY1	chr3:155899207-155899770	SK-N-SH	brain:	n/a	n/a
10	EP300	chr3:155899353-155899709	SK-N-SH_RA	brain:	n/a	n/a
11	CEBPB	chr3:155899380-155899738	IMR90	lung:	n/a	n/a
12	CEBPB	chr3:155899384-155899748	Hela-S3	cervix:	n/a	n/a
13	FOS	chr3:155899258-155899818	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr3:155899333-155899729	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr3:155899381-155899720	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000227709	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1118418	0.93[ASN][1000 genomes]
rs1120745	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11713991	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11915771	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11915832	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11922447	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1353812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs1391889	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1391890	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1499051	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1499052	0.93[ASN][1000 genomes]
rs1499054	0.93[ASN][1000 genomes]
rs1499055	0.82[CEU][hapmap]
rs1499056	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1546229	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17170	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1909372	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1909373	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1909374	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1909375	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1909376	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2173492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3936002	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4234311	0.81[EUR][1000 genomes]
rs4271877	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4333049	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4355235	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4450760	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4453801	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472010	0.89[CEU][hapmap]
rs4488791	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4505650	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4530487	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4533601	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4580504	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4634068	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679763	0.98[ASN][1000 genomes]
rs4679764	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4680238	1.00[JPT][hapmap]
rs4680239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes]
rs4680244	0.88[ASW][hapmap];0.82[CEU][hapmap];0.86[MEX][hapmap]
rs4680249	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441039	0.92[CEU][hapmap]
rs6441042	0.81[MEX][hapmap]
rs6441045	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[ASN][1000 genomes]
rs6441046	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441047	0.93[ASN][1000 genomes]
rs6441049	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441050	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441051	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764861	0.82[ASW][hapmap];0.82[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs6775600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6784723	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6788238	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6806129	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs728382	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7372394	0.93[ASN][1000 genomes]
rs7611194	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7612532	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621586	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625226	0.81[EUR][1000 genomes]
rs7633871	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7634800	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7638421	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7640712	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289962	1.00[JPT][hapmap]
rs963226	0.83[ASW][hapmap];0.82[CEU][hapmap];0.86[MEX][hapmap]
rs963227	0.81[CEU][hapmap]
rs9818040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9832745	0.89[CEU][hapmap]
rs9857202	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9864967	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9866991	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][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	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4577423	SLC33A1	cis	cerebellum	SCAN
rs4577423	SCARNA7	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155870400-155917800	Weak transcription	Aorta	Aorta
2	chr3:155897800-155899800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:155897800-155899800	Enhancers	NHEK	skin
4	chr3:155898400-155899800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:155898400-155899800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:155899400-155904800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:155899400-155905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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