Variant report

Variant	rs17630980
Chromosome Location	chr3:158401554-158401555
allele	A/T
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	FOS	chr3:158401479-158401679	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr3:158401021-158401703	IMR90	lung:	n/a	n/a
3	FOS	chr3:158401488-158401667	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr3:158401378-158401753	IMR90	lung:	n/a	n/a
5	BATF	chr3:158401401-158401618	GM12878	blood:	n/a	chr3:158401534-158401545
6	FOS	chr3:158401434-158401674	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
GFM1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs17630607	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17642769	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17643171	0.82[JPT][hapmap];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[JPT][hapmap];1.00[YRI][hapmap];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[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17699324	1.00[JPT][hapmap];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[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2279562	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2304408	1.00[JPT][hapmap];1.00[YRI][hapmap];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[JPT][hapmap];1.00[YRI][hapmap];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]
rs56089835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs6441208	1.00[JPT][hapmap]
rs6441221	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs6776901	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6777231	1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7610009	1.00[JPT][hapmap];1.00[YRI][hapmap];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
rs17630980	GFM1	cis	Muscle Skeletal	GTEx
rs17630980	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs17630980	GFM1	cis	Nerve Tibial	GTEx
rs17630980	GFM1	cis	Esophagus Mucosa	GTEx
rs17630980	GFM1	cis	Thyroid	GTEx
rs17630980	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs17630980	GFM1	cis	Artery Tibial	GTEx
rs17630980	LXN	cis	multi-tissue	Pritchard

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	chr3:158391000-158402200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:158391000-158402200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:158391000-158402400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:158391000-158403400	Weak transcription	HMEC	breast
32	chr3:158391000-158407800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:158391000-158408000	Weak transcription	Fetal Intestine Large	intestine
34	chr3:158391000-158409000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:158391000-158409600	Weak transcription	Fetal Kidney	kidney
36	chr3:158391000-158413600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:158391000-158418600	Weak transcription	Fetal Brain Male	brain
38	chr3:158391000-158421000	Weak transcription	Fetal Heart	heart
39	chr3:158391000-158427200	Weak transcription	NHEK	skin
40	chr3:158391000-158427400	Weak transcription	Pancreas	Pancrea
41	chr3:158391000-158429200	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:158391000-158430600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:158391200-158401800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:158391200-158410800	Weak transcription	A549	lung
46	chr3:158391600-158412200	Weak transcription	Fetal Intestine Small	intestine
47	chr3:158391800-158410800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr3:158392400-158411400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:158395000-158403600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:158395200-158412400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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