Variant report

Variant	rs1459055
Chromosome Location	chr4:120056815-120056816
allele	C/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	FOSL2	chr4:120056718-120057517	SK-N-SH	brain:	n/a	chr4:120057196-120057205 chr4:120056993-120057004
2	STAT3	chr4:120056734-120057058	MCF10A-Er-Src	breast:	n/a	chr4:120056889-120056897
3	STAT3	chr4:120056732-120057164	MCF10A-Er-Src	breast:	n/a	chr4:120056889-120056897
4	JUND	chr4:120056677-120057421	SK-N-SH	brain:	n/a	chr4:120057196-120057205 chr4:120056993-120057004
5	MEF2A	chr4:120056621-120057450	SK-N-SH	brain:	n/a	chr4:120057197-120057205 chr4:120056930-120056951 chr4:120056934-120056945 chr4:120056928-120056949 chr4:120056928-120056949 chr4:120056935-120056944 chr4:120056931-120056948 chr4:120056930-120056951 chr4:120056933-120056944 chr4:120056932-120056947 chr4:120056933-120056947 chr4:120056928-120056949 chr4:120056932-120056948 chr4:120056931-120056947 chr4:120056935-120056946
6	JUND	chr4:120056671-120057571	SK-N-SH	brain:	n/a	chr4:120057196-120057205 chr4:120056993-120057004
7	MEF2A	chr4:120056620-120057474	SK-N-SH	brain:	n/a	chr4:120057197-120057205 chr4:120056930-120056951 chr4:120056934-120056945 chr4:120056928-120056949 chr4:120056928-120056949 chr4:120056935-120056944 chr4:120056931-120056948 chr4:120056930-120056951 chr4:120056933-120056944 chr4:120056932-120056947 chr4:120056933-120056947 chr4:120056928-120056949 chr4:120056932-120056948 chr4:120056931-120056947 chr4:120056935-120056946
8	TCF12	chr4:120056638-120057549	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
MYOZ2	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1033087	0.88[EUR][1000 genomes]
rs11098486	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11098489	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11098490	0.89[EUR][1000 genomes]
rs11098491	0.89[EUR][1000 genomes]
rs11098492	0.89[EUR][1000 genomes]
rs11729978	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11730138	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11731008	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11733239	0.89[EUR][1000 genomes]
rs11733525	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12508316	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12513191	0.89[EUR][1000 genomes]
rs13111751	0.87[ASN][1000 genomes]
rs13120560	0.89[EUR][1000 genomes]
rs13136593	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2036861	0.88[EUR][1000 genomes]
rs4334737	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4355373	0.89[EUR][1000 genomes]
rs7696877	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9993110	0.89[EUR][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1007214	chr4:120007913-120112460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv1003827	chr4:120008227-120112460	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv522386	chr4:120009147-120115379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
9	nsv1007619	chr4:120014898-120112460	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1459055	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs1459055	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs1459055	BBS7	cis	cerebellum	SCAN
rs1459055	RP11-384K6.6	cis	Whole Blood	GTEx
rs1459055	RP11-384K6.6	cis	Artery Tibial	GTEx
rs1459055	BBS7	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120045200-120059200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:120052000-120057200	Weak transcription	Psoas Muscle	Psoas
3	chr4:120052800-120057000	Weak transcription	Right Ventricle	heart
4	chr4:120052800-120058800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:120052800-120060000	Weak transcription	Fetal Intestine Large	intestine
6	chr4:120053200-120057000	Weak transcription	Left Ventricle	heart
7	chr4:120053200-120057000	Weak transcription	Right Atrium	heart
8	chr4:120053800-120057000	Weak transcription	Aorta	Aorta
9	chr4:120055800-120061800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:120056200-120057000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr4:120056200-120058000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:120056200-120058000	Enhancers	NHDF-Ad	bronchial
13	chr4:120056200-120061200	Enhancers	HSMM	muscle
14	chr4:120056400-120057000	Enhancers	Osteobl	bone
15	chr4:120056400-120057600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:120056400-120057600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:120056400-120057800	Enhancers	HUVEC	blood vessel
18	chr4:120056400-120061800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr4:120056600-120057000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:120056600-120057000	Enhancers	HSMMtube	muscle
21	chr4:120056600-120057400	Enhancers	NH-A	brain
22	chr4:120056600-120058200	Enhancers	Brain Substantia Nigra	brain
23	chr4:120056600-120058800	Enhancers	Brain Hippocampus Middle	brain
24	chr4:120056800-120057000	Enhancers	Brain Anterior Caudate	brain
25	chr4:120056800-120057000	Enhancers	Fetal Muscle Leg	muscle
26	chr4:120056800-120057200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:120056800-120057200	Enhancers	Pancreas	Pancrea
28	chr4:120056800-120057400	Enhancers	HMEC	breast
29	chr4:120056800-120057600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:120056800-120057600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:120056800-120057600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:120056800-120057600	Enhancers	NHLF	lung
33	chr4:120056800-120057800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:120056800-120057800	Enhancers	Brain Angular Gyrus	brain
35	chr4:120056800-120058000	Enhancers	Brain Cingulate Gyrus	brain
36	chr4:120056800-120058000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr4:120056800-120059600	Active TSS	Fetal Muscle Trunk	muscle
38	chr4:120056800-120060200	Active TSS	Fetal Heart	heart
39	chr4:120056800-120060600	Active TSS	Skeletal Muscle Male	skeletal muscle

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