Variant report

Variant	rs62287938
Chromosome Location	chr3:158307024-158307025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs17630607	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17630980	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17697458	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17698494	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17699103	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17699324	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2304408	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28372852	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35057010	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3867391	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55666734	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56075263	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56089835	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56148431	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56167308	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56242377	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60942689	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62286650	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62286654	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288301	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288303	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288305	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288306	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288307	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288344	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288345	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6776901	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6777231	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6804230	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610009	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7628497	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7633713	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62287938	GFM1	cis	Thyroid	GTEx
rs62287938	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs62287938	LXN	cis	multi-tissue	Pritchard
rs62287938	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs62287938	GFM1	cis	Esophagus Mucosa	GTEx
rs62287938	GFM1	cis	Muscle Skeletal	GTEx
rs62287938	GFM1	cis	Artery Tibial	GTEx
rs62287938	GFM1	cis	Nerve Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158290400-158324400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:158292000-158315400	Weak transcription	Right Ventricle	heart
3	chr3:158297800-158312000	Weak transcription	Fetal Heart	heart
4	chr3:158299400-158329400	Weak transcription	Left Ventricle	heart
5	chr3:158299800-158320400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:158301000-158311400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:158302600-158315200	Weak transcription	Fetal Lung	lung
8	chr3:158302600-158316400	Weak transcription	Psoas Muscle	Psoas
9	chr3:158303600-158320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:158304200-158320200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:158304600-158323400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:158305000-158322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:158305600-158330200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:158305800-158328800	Weak transcription	Ovary	ovary

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