Variant report

Variant	rs1620229
Chromosome Location	chr3:158293258-158293259
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	chr3:158293225-158293542	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:158293239-158293531	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158291924..158294331-chr3:158300946..158303373,2	K562	blood:

Variant related genes	Relation type
ENSG00000243150	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1038886	0.84[ASN][1000 genomes]
rs1047366	0.86[ASN][1000 genomes]
rs1075551	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10936158	0.86[ASN][1000 genomes]
rs12107643	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12496174	0.86[ASN][1000 genomes]
rs13074694	0.80[ASN][1000 genomes]
rs13324770	0.82[ASN][1000 genomes]
rs13325932	0.86[ASN][1000 genomes]
rs1369563	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1435642	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1602760	0.84[ASN][1000 genomes]
rs1656374	0.90[AFR][1000 genomes]
rs1656376	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1656377	0.91[ASN][1000 genomes]
rs1714507	0.80[AFR][1000 genomes]
rs1714516	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1714524	0.91[AFR][1000 genomes]
rs17629360	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17629390	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs17629414	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1836688	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1864503	0.86[ASN][1000 genomes]
rs1864507	0.87[ASN][1000 genomes]
rs2115943	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2248924	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276773	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2303909	0.86[ASN][1000 genomes]
rs2364274	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2566344	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2573179	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731118	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2731120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2731122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28481597	0.87[ASN][1000 genomes]
rs2933550	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765025	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3845272	0.88[ASN][1000 genomes]
rs3851361	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3851363	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4680445	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4680449	0.90[ASN][1000 genomes]
rs4680451	0.86[ASN][1000 genomes]
rs4680452	0.86[ASN][1000 genomes]
rs4680453	0.88[ASN][1000 genomes]
rs4680457	0.84[ASN][1000 genomes]
rs4875	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs62287933	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6441212	0.90[ASN][1000 genomes]
rs6441220	0.85[ASN][1000 genomes]
rs6763812	0.85[ASN][1000 genomes]
rs6771248	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6772483	0.84[ASN][1000 genomes]
rs6777711	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6781342	0.86[ASN][1000 genomes]
rs6800914	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6802317	0.86[ASN][1000 genomes]
rs6803047	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6803608	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6804259	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7613814	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7621897	0.84[ASN][1000 genomes]
rs7631310	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7653826	0.90[ASN][1000 genomes]
rs8455	0.88[ASN][1000 genomes]
rs891464	0.88[ASN][1000 genomes]
rs9819567	0.86[ASN][1000 genomes]
rs9819631	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9824985	0.86[ASN][1000 genomes]
rs9844502	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9848908	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9864508	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1013242	chr3:158275578-158305894	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1013112	chr3:158280085-158301728	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1001944	chr3:158280085-158305210	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999408	chr3:158280085-158316431	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1620229	RP11-538P18.2	cis	Artery Tibial	GTEx
rs1620229	MLF1	cis	Esophagus Mucosa	GTEx
rs1620229	GFM1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158290400-158324400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:158291000-158294400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:158292000-158299200	Weak transcription	Left Ventricle	heart
4	chr3:158292000-158315400	Weak transcription	Right Ventricle	heart
5	chr3:158292600-158294000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:158292600-158297200	Enhancers	Fetal Heart	heart
7	chr3:158292800-158293600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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