Variant report

Variant	rs1483685
Chromosome Location	chr4:53702296-53702297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53582996..53584787-chr4:53701412..53703880,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
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];0.85[TSI][hapmap]
rs1043975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[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]
rs1483686	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.92[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]
rs17643154	0.92[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];0.92[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];0.92[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];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2411259	0.80[CEU][hapmap];0.92[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];0.85[TSI][hapmap]
rs301135	0.85[JPT][hapmap];1.00[MEX][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]
rs4864679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.92[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];0.92[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];0.92[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:4 , 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
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1483685	SGCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53691800-53704000	Weak transcription	Right Atrium	heart
2	chr4:53692200-53704000	Weak transcription	Right Ventricle	heart
3	chr4:53698800-53710600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr4:53700000-53702600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr4:53700000-53703000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:53700000-53704800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:53700200-53703000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:53700200-53710800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr4:53700400-53702400	Weak transcription	Ovary	ovary
10	chr4:53700400-53709600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:53700600-53703800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:53700800-53702400	Weak transcription	Fetal Heart	heart
13	chr4:53700800-53702800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:53700800-53702800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:53700800-53702800	Weak transcription	HSMM	muscle
16	chr4:53700800-53703800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:53700800-53703800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:53700800-53704000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:53700800-53704000	Weak transcription	Osteobl	bone
20	chr4:53701000-53702400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:53701000-53702400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:53701000-53702400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:53701000-53702400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:53701000-53702600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:53701000-53703200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:53701000-53704000	Weak transcription	Esophagus	oesophagus
27	chr4:53701000-53704000	Weak transcription	Left Ventricle	heart
28	chr4:53701000-53704000	Weak transcription	Psoas Muscle	Psoas
29	chr4:53701000-53706800	Weak transcription	Stomach Mucosa	stomach
30	chr4:53701000-53707000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:53701000-53707800	Weak transcription	Aorta	Aorta
32	chr4:53701400-53702400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:53701400-53702400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:53701400-53703600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:53701600-53702400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:53701600-53702600	Weak transcription	NHEK	skin
37	chr4:53701600-53704200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:53701600-53704600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr4:53701800-53703000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:53702000-53702400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:53702200-53702400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:53702200-53703600	Enhancers	HMEC	breast
43	chr4:53702200-53704000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:53702200-53705800	Enhancers	NHDF-Ad	bronchial

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