Variant report

Variant	rs56089835
Chromosome Location	chr3:158401032-158401033
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr3:158400949-158401388	K562	blood:	n/a	n/a
2	MAFK	chr3:158401024-158401389	HepG2	liver:	n/a	n/a
3	MAFK	chr3:158401021-158401703	IMR90	lung:	n/a	n/a
4	MAFF	chr3:158401032-158401380	HepG2	liver:	n/a	chr3:158401204-158401222
5	MAFF	chr3:158401030-158401402	K562	blood:	n/a	chr3:158401204-158401222
6	MAFK	chr3:158401032-158401360	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GFM1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:50)

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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642769	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17643171	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17643252	0.80[EUR][1000 genomes]
rs17643483	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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17699478	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17699526	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17699997	0.80[EUR][1000 genomes]
rs17700122	0.80[EUR][1000 genomes]
rs2279561	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2279562	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2304408	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2307064	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28372852	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075263	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56148431	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56152025	0.80[EUR][1000 genomes]
rs56167308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56242377	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60942689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794798	0.80[EUR][1000 genomes]
rs61794799	0.80[EUR][1000 genomes]
rs62286647	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[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];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62286654	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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]
rs62288303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62288345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441221	0.80[EUR][1000 genomes]
rs6776901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6777231	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6783610	0.80[EUR][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];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs56089835	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs56089835	LXN	cis	multi-tissue	Pritchard
rs56089835	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs56089835	GFM1	cis	Thyroid	GTEx
rs56089835	GFM1	cis	Muscle Skeletal	GTEx
rs56089835	GFM1	cis	Artery Tibial	GTEx
rs56089835	GFM1	cis	Nerve Tibial	GTEx
rs56089835	GFM1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158386200-158407800	Weak transcription	HepG2	liver
2	chr3:158390200-158402800	Weak transcription	HSMM	muscle
3	chr3:158390400-158416800	Weak transcription	Aorta	Aorta
4	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:158390600-158410600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:158390600-158427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:158390800-158407800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:158390800-158407800	Weak transcription	Small Intestine	intestine
9	chr3:158390800-158408000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:158390800-158408000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:158390800-158408000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:158390800-158408200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:158390800-158408200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:158390800-158410800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:158390800-158416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:158390800-158425400	Weak transcription	Fetal Brain Female	brain
17	chr3:158390800-158427000	Weak transcription	Brain Angular Gyrus	brain
18	chr3:158390800-158427400	Weak transcription	Esophagus	oesophagus
19	chr3:158390800-158427400	Weak transcription	Lung	lung
20	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
24	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
25	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
26	chr3:158390800-158444200	Weak transcription	Gastric	stomach
27	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:158391000-158401400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:158391000-158401400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:158391000-158402200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:158391000-158402200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:158391000-158402400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:158391000-158403400	Weak transcription	HMEC	breast
34	chr3:158391000-158407800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:158391000-158408000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:158391000-158409000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:158391000-158409600	Weak transcription	Fetal Kidney	kidney
38	chr3:158391000-158413600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:158391000-158418600	Weak transcription	Fetal Brain Male	brain
40	chr3:158391000-158421000	Weak transcription	Fetal Heart	heart
41	chr3:158391000-158427200	Weak transcription	NHEK	skin
42	chr3:158391000-158427400	Weak transcription	Pancreas	Pancrea
43	chr3:158391000-158429200	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:158391000-158430600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:158391200-158401800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:158391200-158410800	Weak transcription	A549	lung
48	chr3:158391600-158412200	Weak transcription	Fetal Intestine Small	intestine
49	chr3:158391800-158410800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:158392400-158411400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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