Variant report

Variant	rs12431578
Chromosome Location	chr14:21957934-21957935
allele	A/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	chr14:21957868-21958403	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:21956681..21958575-chr14:21959135..21961064,2	MCF-7	breast:
2	chr14:21941797..21947093-chr14:21954513..21961521,11	MCF-7	breast:

Variant related genes	Relation type
TOX4	TF binding region
ENSG00000129472	Chromatin interaction
ENSG00000092203	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10135215	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1060722	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11156994	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1139130	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12435421	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1263793	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1263796	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1263799	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1263801	0.82[AMR][1000 genomes]
rs12880402	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12889546	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2297093	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28526734	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28608673	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28694613	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3737049	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4296176	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7150948	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8004916	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs933192	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs966602	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3518898	chr14:21805983-22077584	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv3518899	chr14:21805983-22077584	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1054013	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541991	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv530011	chr14:21876973-21985341	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2422459	chr14:21931624-22169502	Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12431578	METTL3	Cis_1M	lymphoblastoid	RTeQTL
rs12431578	TOX4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21946000-21960600	Weak transcription	Small Intestine	intestine
2	chr14:21946200-21977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:21946400-21958000	Weak transcription	Pancreas	Pancrea
4	chr14:21946400-21958800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:21946400-21960800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:21946400-21971400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr14:21946600-21958000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr14:21946600-21960400	Weak transcription	Stomach Mucosa	stomach
9	chr14:21946600-21960800	Weak transcription	Aorta	Aorta
10	chr14:21946800-21959000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr14:21946800-21959000	Weak transcription	Fetal Brain Male	brain
12	chr14:21946800-21960800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr14:21947000-21978000	Weak transcription	Fetal Heart	heart
14	chr14:21954600-21967000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr14:21954600-21972600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr14:21954800-21959200	Strong transcription	Primary T cells from cord blood	blood
17	chr14:21954800-21961400	Strong transcription	Rectal Smooth Muscle	rectum
18	chr14:21954800-21966600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr14:21954800-21967000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:21954800-21967000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr14:21954800-21971400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:21954800-21972000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr14:21954800-21972000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr14:21954800-21972200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr14:21954800-21972200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr14:21954800-21977400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr14:21955000-21967000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr14:21955000-21972000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr14:21955000-21972400	Strong transcription	Fetal Thymus	thymus
30	chr14:21955200-21963400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr14:21955200-21966800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr14:21955200-21972000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr14:21955200-21972200	Strong transcription	Liver	Liver
34	chr14:21955200-21972600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr14:21955400-21964000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr14:21955400-21966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr14:21955400-21966600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr14:21955400-21967000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr14:21955400-21967400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:21955400-21971400	Strong transcription	Placenta	Placenta
41	chr14:21955400-21971600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr14:21955400-21972000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:21955400-21972000	Strong transcription	Fetal Intestine Large	intestine
44	chr14:21955400-21972000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr14:21955400-21972200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr14:21955400-21972200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr14:21955400-21972200	Strong transcription	Brain Anterior Caudate	brain
48	chr14:21955400-21972600	Strong transcription	Dnd41	blood
49	chr14:21955600-21958200	Strong transcription	NHLF	lung
50	chr14:21955600-21959000	Strong transcription	Colon Smooth Muscle	Colon

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