Variant report

Variant	rs12458548
Chromosome Location	chr18:29667144-29667145
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	POLR2A	chr18:29667003-29667203	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr18:29666738-29667308	HCT-116	colon:	n/a	n/a
3	SP1	chr18:29666663-29667312	HCT-116	colon:	n/a	n/a
4	FOS	chr18:29666822-29667205	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr18:29666797-29667225	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr18:29666801-29667243	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr18:29666676-29667257	HCT-116	colon:	n/a	n/a
8	TEAD4	chr18:29666767-29667197	HCT-116	colon:	n/a	n/a
9	FOSL1	chr18:29666750-29667175	HCT-116	colon:	n/a	n/a
10	FOS	chr18:29666870-29667188	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr18:29666807-29667278	MCF10A-Er-Src	breast:	n/a	n/a
12	SP1	chr18:29666666-29667316	HCT-116	colon:	n/a	n/a
13	CEBPB	chr18:29666930-29667284	IMR90	lung:	n/a	n/a
14	FOSL1	chr18:29666736-29667301	HCT-116	colon:	n/a	n/a
15	STAT3	chr18:29666807-29667238	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:29662644..29667608-chr18:29668028..29673014,9	K562	blood:
2	chr18:29660336..29661951-chr18:29664954..29667841,2	K562	blood:
3	chr18:29666841..29669333-chr18:29671631..29673559,3	MCF-7	breast:

Variant related genes	Relation type
RNF138	TF binding region
ENSG00000134758	Chromatin interaction
ENSG00000265008	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11081741	0.82[EUR][1000 genomes]
rs11081746	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11663563	0.82[AMR][1000 genomes]
rs12455044	0.85[AFR][1000 genomes]
rs12458837	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12458851	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1808891	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2048245	0.82[AMR][1000 genomes]
rs3760568	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4799326	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4799629	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4799632	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62093949	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62093950	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7238559	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9676102	0.80[EUR][1000 genomes]
rs993897	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757673	chr18:29632749-29674992	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2758719	chr18:29632749-29674992	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv909521	chr18:29645496-29671510	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv909522	chr18:29645496-29674992	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv909523	chr18:29645496-29679922	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1055457	chr18:29654978-29677371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12458548	RNF138	Cis_1M	lymphoblastoid	RTeQTL
rs12458548	RNF138	cis	Esophagus Mucosa	GTEx
rs12458548	RNF138	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29631400-29671400	Weak transcription	Hela-S3	cervix
2	chr18:29656000-29671400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr18:29663800-29671400	Weak transcription	Fetal Kidney	kidney
4	chr18:29664400-29671400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:29664600-29667600	Enhancers	NHEK	skin
6	chr18:29664600-29671600	Weak transcription	Left Ventricle	heart
7	chr18:29665200-29671400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr18:29665200-29671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:29665400-29667600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr18:29665400-29671400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr18:29665600-29671400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:29665600-29671400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr18:29665800-29668000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr18:29666000-29667200	Enhancers	Stomach Mucosa	stomach
15	chr18:29666000-29667600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr18:29666000-29667800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr18:29666000-29667800	Enhancers	Primary B cells from cord blood	blood
18	chr18:29666000-29670800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr18:29666000-29671400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr18:29666000-29671400	Weak transcription	NHDF-Ad	bronchial
21	chr18:29666200-29668200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr18:29666200-29670800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr18:29666200-29671400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr18:29666200-29671400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr18:29666200-29671400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:29666400-29667400	Enhancers	Fetal Muscle Leg	muscle
27	chr18:29666400-29670800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr18:29666400-29670800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr18:29666400-29671000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr18:29666400-29671200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr18:29666400-29671200	Weak transcription	HUVEC	blood vessel
32	chr18:29666400-29671400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr18:29666400-29671400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr18:29666400-29671400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr18:29666400-29671400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr18:29666400-29671400	Weak transcription	Adipose Nuclei	Adipose
37	chr18:29666400-29671400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr18:29666400-29671400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr18:29666400-29671400	Weak transcription	Thymus	Thymus
40	chr18:29666400-29671400	Weak transcription	Dnd41	blood
41	chr18:29666600-29670800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr18:29666600-29671000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr18:29666600-29671200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr18:29666600-29671200	Weak transcription	Fetal Thymus	thymus
45	chr18:29666600-29671400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr18:29666600-29671400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr18:29666600-29671400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr18:29666600-29671400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr18:29666800-29667400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr18:29666800-29667400	Weak transcription	Spleen	Spleen

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