Variant report

Variant	rs4243628
Chromosome Location	chr14:64853672-64853673
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:64853659-64856145	GM12892	blood:	n/a	n/a
2	POLR2A	chr14:64853564-64856071	GM12892	blood:	n/a	n/a
3	POLR2A	chr14:64853577-64855994	GM12892	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:64853586..64859592-chr14:64968792..64973445,7	MCF-7	breast:
2	chr14:64852241..64854032-chr14:64855685..64858299,2	K562	blood:
3	chr14:64853592..64856673-chr14:64970174..64974352,5	K562	blood:
4	chr14:64853142..64856847-chr14:64968558..64973163,8	K562	blood:
5	chr14:64853000..64857077-chr14:64970157..64972159,5	MCF-7	breast:
6	chr14:64849072..64851783-chr14:64852563..64854681,2	K562	blood:
7	chr14:64803480..64807605-chr14:64853546..64855883,4	K562	blood:

No data

Variant related genes	Relation type
MTHFD1	TF binding region
ENSG00000126804	Chromatin interaction
ENSG00000214770	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000140009	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12434608	0.94[EUR][1000 genomes]
rs1256093	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256095	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1256097	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1256099	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1256100	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1256101	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1256102	0.84[EUR][1000 genomes]
rs1256107	0.84[EUR][1000 genomes]
rs1256108	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1256109	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1256111	0.84[EUR][1000 genomes]
rs1256112	0.85[ASN][1000 genomes]
rs1256113	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1262246	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1270057	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12886138	0.86[ASN][1000 genomes]
rs12889097	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12894546	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35020344	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36016358	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4243628	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs4243628	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs4243628	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx
rs4243628	ESR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64839200-64853800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:64844200-64854000	Weak transcription	Ovary	ovary
3	chr14:64849400-64854000	Weak transcription	Small Intestine	intestine
4	chr14:64851400-64853800	Weak transcription	NHLF	lung
5	chr14:64852200-64854000	Enhancers	Fetal Heart	heart
6	chr14:64852600-64853800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr14:64852600-64857000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr14:64852800-64853800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr14:64852800-64853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr14:64852800-64853800	Weak transcription	Hela-S3	cervix
11	chr14:64852800-64854000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:64852800-64856800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr14:64853000-64857000	Active TSS	K562	blood
14	chr14:64853200-64853800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:64853200-64853800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:64853200-64853800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr14:64853200-64853800	Enhancers	Primary hematopoietic stem cells	blood
18	chr14:64853200-64853800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:64853200-64853800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:64853200-64853800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr14:64853200-64853800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr14:64853200-64853800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:64853200-64853800	Enhancers	Brain Germinal Matrix	brain
24	chr14:64853200-64853800	Enhancers	Fetal Thymus	thymus
25	chr14:64853200-64853800	Enhancers	HepG2	liver
26	chr14:64853200-64853800	Enhancers	HMEC	breast
27	chr14:64853200-64853800	Active TSS	NHEK	skin
28	chr14:64853200-64854000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr14:64853200-64854000	Enhancers	Fetal Brain Male	brain
30	chr14:64853200-64854000	Enhancers	Left Ventricle	heart
31	chr14:64853200-64854000	Enhancers	Psoas Muscle	Psoas
32	chr14:64853200-64855400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:64853200-64856600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr14:64853200-64856600	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr14:64853200-64856800	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr14:64853400-64853800	Enhancers	Primary B cells from cord blood	blood
37	chr14:64853400-64853800	Enhancers	Primary B cells from peripheral blood	blood
38	chr14:64853400-64853800	Enhancers	Dnd41	blood
39	chr14:64853400-64854000	Active TSS	GM12878-XiMat	blood
40	chr14:64853400-64856600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr14:64853400-64857000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr14:64853600-64853800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr14:64853600-64853800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr14:64853600-64853800	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr14:64853600-64853800	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr14:64853600-64853800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:64853600-64853800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr14:64853600-64853800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr14:64853600-64853800	Enhancers	Brain Anterior Caudate	brain
50	chr14:64853600-64853800	Enhancers	Brain Hippocampus Middle	brain

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