Variant report

Variant	rs4680466
Chromosome Location	chr3:158500698-158500699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFM1-4	chr3:158500336-158500913	ENSG00000271778.1

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1381462	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1381464	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1548013	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1985781	0.83[AFR][1000 genomes]
rs3755746	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816637	0.87[AFR][1000 genomes]
rs4680461	0.96[ASN][1000 genomes]
rs4680463	0.93[ASN][1000 genomes]
rs56070013	0.83[AFR][1000 genomes]
rs61461024	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73158358	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429899	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7616425	0.89[ASN][1000 genomes]
rs7617706	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620380	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9290028	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9810241	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811858	0.92[ASN][1000 genomes]
rs9825140	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9849301	0.92[ASN][1000 genomes]
rs9857480	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9859969	0.83[AFR][1000 genomes]
rs9861289	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9861622	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680466	GFM1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158486800-158518200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:158488400-158501000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:158489200-158508800	Weak transcription	Primary T cells from cord blood	blood
4	chr3:158490000-158501000	Weak transcription	Ovary	ovary
5	chr3:158492200-158510600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:158493800-158501400	Weak transcription	Fetal Stomach	stomach
7	chr3:158494600-158501000	Weak transcription	Right Atrium	heart
8	chr3:158494600-158504600	Weak transcription	Left Ventricle	heart
9	chr3:158495400-158505600	Weak transcription	Colonic Mucosa	Colon
10	chr3:158495600-158501200	Weak transcription	Small Intestine	intestine
11	chr3:158495600-158504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:158495600-158508600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:158495800-158501000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:158496000-158506000	Weak transcription	Osteobl	bone
15	chr3:158498400-158501600	Enhancers	Fetal Intestine Large	intestine
16	chr3:158498600-158501200	Enhancers	Fetal Intestine Small	intestine
17	chr3:158499000-158501600	Enhancers	Fetal Lung	lung
18	chr3:158499200-158501600	Enhancers	Colon Smooth Muscle	Colon
19	chr3:158499400-158501600	Enhancers	Fetal Kidney	kidney
20	chr3:158499600-158501600	Enhancers	Rectal Smooth Muscle	rectum
21	chr3:158499800-158501200	Enhancers	A549	lung
22	chr3:158500000-158501600	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:158500200-158500800	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr3:158500200-158501400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr3:158500400-158501000	Enhancers	NHLF	lung
26	chr3:158500400-158501600	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr3:158500600-158501400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr3:158500600-158501800	Enhancers	Stomach Smooth Muscle	stomach

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