Variant report

Variant	rs2542148
Chromosome Location	chr18:12777573-12777574
allele	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	POLR2A	chr18:12777480-12777619	MCF10A-Er-Src	breast:	n/a	n/a
2	BACH1	chr18:12777541-12777884	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr18:12776956-12777913	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr18:12777507-12777723	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000260302	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11663253	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1893217	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2014857	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2542147	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542149	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542150	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542151	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847259	1.00[ASN][1000 genomes]
rs2847260	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847274	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847278	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847280	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847293	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34920518	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs45450798	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60474474	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60735058	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60751993	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7237497	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8096138	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs888270	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952749	0.81[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1062149	chr18:12728115-12783898	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
9	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2542148	RP11-973H7.1	cis	lung	GTEx
rs2542148	RP11-973H7.1	cis	Artery Tibial	GTEx
rs2542148	RP11-973H7.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12767400-12815800	Weak transcription	Gastric	stomach
2	chr18:12774800-12777600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr18:12775000-12778000	ZNF genes & repeats	Fetal Thymus	thymus
4	chr18:12776000-12793600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr18:12776200-12785800	Weak transcription	Primary T cells from cord blood	blood
6	chr18:12776200-12791600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr18:12776200-12792600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr18:12776200-12794000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr18:12776200-12800800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr18:12776400-12800000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr18:12776600-12777800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:12776600-12778200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr18:12776800-12777600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr18:12776800-12777600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr18:12776800-12777600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr18:12776800-12777600	Bivalent/Poised TSS	Fetal Stomach	stomach
19	chr18:12776800-12777800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:12776800-12778000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr18:12776800-12778000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr18:12776800-12778000	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr18:12776800-12778000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:12776800-12778200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr18:12776800-12788600	Weak transcription	Dnd41	blood
26	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr18:12777000-12777800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr18:12777000-12777800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:12777000-12778000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr18:12777200-12777600	Active TSS	Primary T cells fromperipheralblood	blood
31	chr18:12777200-12777600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr18:12777200-12777600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr18:12777200-12777800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr18:12777200-12777800	Active TSS	Colonic Mucosa	Colon
35	chr18:12777200-12777800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr18:12777200-12777800	Active TSS	Fetal Muscle Leg	muscle
37	chr18:12777200-12777800	Active TSS	Placenta	Placenta
38	chr18:12777200-12777800	Active TSS	Monocytes-CD14+_RO01746	blood
39	chr18:12777200-12778000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:12777200-12778000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr18:12777200-12778000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr18:12777200-12778000	Active TSS	Fetal Brain Female	brain
43	chr18:12777200-12778000	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr18:12777200-12778000	ZNF genes & repeats	Thymus	Thymus
45	chr18:12777400-12777600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
46	chr18:12777400-12777600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr18:12777400-12777800	Active TSS	Liver	Liver
48	chr18:12777400-12777800	Active TSS	Stomach Smooth Muscle	stomach
49	chr18:12777400-12778000	Enhancers	Lung	lung
50	chr18:12777400-12778200	Active TSS	Fetal Intestine Small	intestine

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