Variant report

Variant	rs4864679
Chromosome Location	chr4:53697746-53697747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53696996..53699820-chr4:53703749..53706147,2	MCF-7	breast:
2	chr4:53690322..53693293-chr4:53696846..53698754,2	MCF-7	breast:
3	chr4:53697493..53701667-chr4:53702709..53704806,3	MCF-7	breast:
4	chr4:53586478..53588688-chr4:53694874..53697791,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248375	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10000595	0.86[TSI][hapmap]
rs10001855	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10008073	0.86[CEU][hapmap];0.93[CHB][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10014464	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10026175	0.89[CEU][hapmap]
rs10028567	0.89[CEU][hapmap];0.92[TSI][hapmap]
rs1043975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1047959	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10866413	0.93[JPT][hapmap]
rs11930907	0.84[ASN][1000 genomes]
rs11934293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941562	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1483685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483686	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1483687	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17082081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17082143	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17082147	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17613967	0.84[TSI][hapmap]
rs17643154	1.00[TSI][hapmap]
rs1963003	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003198	0.84[ASN][1000 genomes]
rs2017237	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2046364	0.85[ASN][1000 genomes]
rs2062253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2200226	0.87[ASN][1000 genomes]
rs2279334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306601	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2411259	0.80[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2411281	0.83[ASN][1000 genomes]
rs28419463	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28454903	0.81[EUR][1000 genomes]
rs28489424	0.81[EUR][1000 genomes]
rs28526700	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28704139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28733375	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28735908	0.81[EUR][1000 genomes]
rs28811693	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2898681	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs301119	0.86[JPT][hapmap]
rs301123	0.84[CHB][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs301135	0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs301136	0.80[AMR][1000 genomes]
rs4242020	0.81[EUR][1000 genomes]
rs4309903	0.81[EUR][1000 genomes]
rs4864673	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864681	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864688	0.85[ASN][1000 genomes]
rs4864690	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4864691	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4865422	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4990628	0.81[EUR][1000 genomes]
rs5012592	0.89[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs59649036	0.85[ASN][1000 genomes]
rs61268502	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62336785	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62336788	0.97[EUR][1000 genomes]
rs62336791	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336792	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336794	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62336795	0.86[ASN][1000 genomes]
rs62336823	0.81[ASN][1000 genomes]
rs62338801	0.81[EUR][1000 genomes]
rs62338805	0.81[EUR][1000 genomes]
rs6833096	0.84[ASN][1000 genomes]
rs6839084	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6852148	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs73143042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900607	0.87[ASN][1000 genomes]
rs922932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs922933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9646	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9993034	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4864679	SGCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53691200-53698800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:53691600-53698600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:53691600-53698800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:53691800-53698800	Weak transcription	Left Ventricle	heart
5	chr4:53691800-53704000	Weak transcription	Right Atrium	heart
6	chr4:53692200-53700400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:53692200-53704000	Weak transcription	Right Ventricle	heart
8	chr4:53692400-53700000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:53692400-53700200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:53692400-53700200	Weak transcription	Psoas Muscle	Psoas
11	chr4:53693000-53698600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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