Variant report

Variant	rs1602760
Chromosome Location	chr3:158395670-158395671
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: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1038886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1047366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1075551	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10936158	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12107643	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12496174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639052	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13074694	0.93[ASN][1000 genomes]
rs13324770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13325932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1369563	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1435642	0.86[ASN][1000 genomes]
rs1620229	0.84[ASN][1000 genomes]
rs1714516	0.84[ASN][1000 genomes]
rs17629360	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17629390	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17629414	0.82[ASN][1000 genomes]
rs1836688	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1864503	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864507	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2115943	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2248924	0.87[ASN][1000 genomes]
rs2276773	0.81[ASN][1000 genomes]
rs2303909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2364274	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2566344	0.86[ASN][1000 genomes]
rs2573179	0.86[ASN][1000 genomes]
rs2731112	0.84[ASN][1000 genomes]
rs2731118	0.86[ASN][1000 genomes]
rs2731120	0.82[ASN][1000 genomes]
rs2731122	0.86[ASN][1000 genomes]
rs28481597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2933550	0.84[ASN][1000 genomes]
rs3765025	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3845272	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3851361	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851363	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680445	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4680449	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680450	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680452	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680453	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4875	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62287933	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6441212	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771248	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6772483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777711	0.84[ASN][1000 genomes]
rs6781342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6800914	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6802317	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6803047	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803608	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6804259	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7609717	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7613814	0.81[ASN][1000 genomes]
rs7621897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7631310	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7653826	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8455	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs891464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9819567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9819631	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9824985	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9844502	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9848908	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9864508	0.80[AMR][1000 genomes];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1602760	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs1602760	MLF1	cis	Esophagus Mucosa	GTEx
rs1602760	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs1602760	MLF1	cis	Heart Left Ventricle	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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