Variant report

Variant	rs62288303
Chromosome Location	chr3:158395677-158395678
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	chr3:158388750..158391682-chr3:158392394..158395997,3	K562	blood:

Variant related genes	Relation type
ENSG00000079257	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs17630607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17630980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642769	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17643171	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17697458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17699478	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17699526	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2279561	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2279562	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2304408	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2307064	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28372852	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35057010	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3867391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55666734	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075263	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56089835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56148431	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56167308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56242377	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60942689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62286647	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62286649	0.80[ASN][1000 genomes]
rs62286650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62286654	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62287938	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62288301	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6777231	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804230	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7610009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62288303	GFM1	cis	Artery Tibial	GTEx
rs62288303	GFM1	cis	Nerve Tibial	GTEx
rs62288303	GFM1	cis	Esophagus Mucosa	GTEx
rs62288303	GFM1	cis	Thyroid	GTEx
rs62288303	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs62288303	LXN	cis	multi-tissue	Pritchard
rs62288303	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs62288303	GFM1	cis	Muscle Skeletal	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158386200-158407800	Weak transcription	HepG2	liver
2	chr3:158389400-158396200	Weak transcription	K562	blood
3	chr3:158390200-158397600	Weak transcription	HSMMtube	muscle
4	chr3:158390200-158402800	Weak transcription	HSMM	muscle
5	chr3:158390400-158401000	Weak transcription	NHDF-Ad	bronchial
6	chr3:158390400-158416800	Weak transcription	Aorta	Aorta
7	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:158390600-158397400	Weak transcription	NH-A	brain
9	chr3:158390600-158410600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:158390800-158395800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:158390800-158396200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:158390800-158396200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:158390800-158396200	Weak transcription	Ovary	ovary
15	chr3:158390800-158396200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:158390800-158396600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:158390800-158397000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:158390800-158397400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:158390800-158400000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:158390800-158407800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:158390800-158407800	Weak transcription	Small Intestine	intestine
22	chr3:158390800-158408000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:158390800-158408000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:158390800-158408000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:158390800-158408200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:158390800-158408200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:158390800-158410800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:158390800-158416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:158390800-158425400	Weak transcription	Fetal Brain Female	brain
30	chr3:158390800-158427000	Weak transcription	Brain Angular Gyrus	brain
31	chr3:158390800-158427400	Weak transcription	Esophagus	oesophagus
32	chr3:158390800-158427400	Weak transcription	Lung	lung
33	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
37	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
38	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
39	chr3:158390800-158444200	Weak transcription	Gastric	stomach
40	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:158391000-158395800	Weak transcription	Primary B cells from cord blood	blood
42	chr3:158391000-158396000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:158391000-158396200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:158391000-158396200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:158391000-158396200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:158391000-158396200	Weak transcription	Fetal Lung	lung
47	chr3:158391000-158396400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:158391000-158396400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:158391000-158396600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:158391000-158396800	Weak transcription	NHLF	lung

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