Variant report

Variant	rs4680450
Chromosome Location	chr3:158374017-158374018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158366809..158369003-chr3:158371000..158374094,3	MCF-7	breast:
2	chr3:158370276..158374326-chr3:158374803..158381339,9	K562	blood:
3	chr3:158361802..158369104-chr3:158370015..158376189,12	K562	blood:
4	chr3:158373925..158377040-chr3:158384143..158388080,3	K562	blood:
5	chr3:158361174..158366807-chr3:158367896..158374332,10	K562	blood:

Variant related genes	Relation type
ENSG00000079257	Chromatin interaction
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1038886	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1047366	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1075551	0.81[ASN][1000 genomes]
rs10936158	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12107643	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12496174	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12639052	0.87[EUR][1000 genomes]
rs13074694	0.85[ASN][1000 genomes]
rs13324770	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13325932	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1602760	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1836688	0.84[ASN][1000 genomes]
rs1864503	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864507	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2115943	0.81[ASN][1000 genomes]
rs2248924	0.86[ASN][1000 genomes]
rs2303909	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2364274	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2566344	0.85[ASN][1000 genomes]
rs2573179	0.85[ASN][1000 genomes]
rs2731118	0.85[ASN][1000 genomes]
rs2731120	0.81[ASN][1000 genomes]
rs28481597	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2933550	0.84[ASN][1000 genomes]
rs3765025	0.84[ASN][1000 genomes]
rs3845272	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3851361	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3851363	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680449	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4680451	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680452	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680453	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680457	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4875	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441212	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441220	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6763812	0.80[ASN][1000 genomes]
rs6771248	0.84[ASN][1000 genomes]
rs6772483	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6777711	0.80[ASN][1000 genomes]
rs6781342	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800914	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6802317	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6803047	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6803608	0.84[ASN][1000 genomes]
rs6804259	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7609717	0.88[AMR][1000 genomes]
rs7621897	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7631310	0.81[ASN][1000 genomes]
rs7653826	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8455	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs891464	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9819567	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824985	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9844502	0.81[ASN][1000 genomes]
rs9848908	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4680450	GFM1	cis	cerebellar cortex	BrainEAC
rs4680450	GFM1	cis	temporal cortex	BrainEAC
rs4680450	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs4680450	GFM1	cis	brain	BrainEAC
rs4680450	GFM1	cis	intralobular white matter	BrainEAC
rs4680450	MLF1	cis	Heart Left Ventricle	GTEx
rs4680450	LXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158362800-158389600	Weak transcription	Gastric	stomach
2	chr3:158362800-158389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:158362800-158390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:158363000-158376600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:158363000-158378200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:158363000-158379800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:158363000-158381800	Weak transcription	Esophagus	oesophagus
8	chr3:158363200-158378600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:158363200-158389400	Weak transcription	Fetal Brain Male	brain
10	chr3:158363400-158374200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:158363400-158376600	Weak transcription	Fetal Kidney	kidney
12	chr3:158363600-158376600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:158363600-158379000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:158363600-158389400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:158363800-158374800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:158363800-158375000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:158363800-158375800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:158363800-158388200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:158363800-158388600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:158364000-158374800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:158364000-158375000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:158364000-158375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:158364000-158375200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:158364000-158375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:158364000-158377600	Strong transcription	Osteobl	bone
26	chr3:158364000-158385400	Weak transcription	Fetal Heart	heart
27	chr3:158364000-158387400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:158364000-158388400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:158364200-158374600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:158364200-158375200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:158364200-158377200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:158364200-158378600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:158364200-158379000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:158364200-158385800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:158364200-158388200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:158364400-158374200	Strong transcription	A549	lung
37	chr3:158364400-158377800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:158364400-158388600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:158364600-158374600	Strong transcription	Liver	Liver
40	chr3:158364600-158374800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr3:158364800-158374600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:158364800-158380400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:158364800-158388000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:158364800-158391000	Strong transcription	Dnd41	blood
45	chr3:158365400-158374800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:158365400-158374800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:158365400-158375000	Strong transcription	Fetal Thymus	thymus
48	chr3:158365600-158375800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:158365800-158374800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:158365800-158378800	Weak transcription	Colon Smooth Muscle	Colon

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