Variant report

Variant	rs6804259
Chromosome Location	chr3:158323212-158323213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1038886	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1047366	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1075551	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936158	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107643	1.00[CHB][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496174	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12639052	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13074694	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs13324770	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13325932	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1369563	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1435642	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1435643	0.85[CHB][hapmap]
rs1595028	0.95[CHB][hapmap]
rs15967	0.81[ASN][1000 genomes]
rs1602760	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1620229	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1656366	0.95[CHB][hapmap]
rs1656376	0.95[CHB][hapmap];0.90[YRI][hapmap]
rs1656377	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1714507	0.95[CHB][hapmap];0.85[YRI][hapmap]
rs1714516	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1714518	0.95[CHB][hapmap]
rs17629360	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17629390	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17629414	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630086	0.85[CHB][hapmap]
rs17699456	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs1836688	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1864503	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864507	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2115943	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2248924	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2276773	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303909	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2364274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2566344	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2573179	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2731112	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2731118	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2731120	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2731122	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28481597	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2933550	0.96[ASN][1000 genomes]
rs3765025	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3845272	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851362	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3851363	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680445	0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680449	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680450	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680451	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680452	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680453	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680457	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4875	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs62287933	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289789	0.81[ASN][1000 genomes]
rs6441206	0.95[CHB][hapmap]
rs6441212	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441220	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6763812	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6771248	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772483	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777711	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781342	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795376	0.95[CHB][hapmap]
rs6800914	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6802317	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6803047	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6803608	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6804249	0.80[YRI][hapmap]
rs7612250	0.85[CHB][hapmap]
rs7612520	0.81[ASN][1000 genomes]
rs7613814	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613824	0.84[CHB][hapmap]
rs7620927	0.95[CHB][hapmap]
rs7621897	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628293	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs7631310	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7635993	0.80[YRI][hapmap]
rs7647356	0.81[ASN][1000 genomes]
rs7648618	0.90[CHB][hapmap]
rs7653826	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8455	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891464	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9810887	0.90[CHB][hapmap]
rs9819134	0.90[CHB][hapmap]
rs9819567	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819631	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9824985	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9844502	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9848908	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858318	0.90[CHB][hapmap]
rs9859129	0.90[CHB][hapmap]
rs9864508	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883657	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6804259	LXN	cis	multi-tissue	Pritchard
rs6804259	MLF1	cis	Heart Left Ventricle	GTEx
rs6804259	MLF1	cis	Esophagus Mucosa	GTEx
rs6804259	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs6804259	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs6804259	GFM1	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158290400-158324400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:158299400-158329400	Weak transcription	Left Ventricle	heart
3	chr3:158304600-158323400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:158305600-158330200	Weak transcription	Brain Anterior Caudate	brain
5	chr3:158305800-158328800	Weak transcription	Ovary	ovary
6	chr3:158311400-158329800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:158314200-158324400	Weak transcription	NHDF-Ad	bronchial
8	chr3:158315600-158324600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:158316000-158326400	Weak transcription	Right Ventricle	heart
10	chr3:158316800-158324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:158318800-158324000	Weak transcription	Adipose Nuclei	Adipose
12	chr3:158318800-158325200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:158320400-158323400	Weak transcription	Fetal Stomach	stomach
14	chr3:158320400-158323800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:158320800-158324600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:158321400-158325800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:158321600-158323800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:158322200-158324800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:158322400-158324000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:158322600-158326000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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