Variant report

Variant	rs7340453
Chromosome Location	chr2:74428015-74428016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74357697..74362841-chr2:74424131..74428670,5	K562	blood:
2	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
3	chr2:74427072..74428786-chr2:74464824..74466711,2	K562	blood:
4	chr2:74373671..74376054-chr2:74427539..74429224,2	MCF-7	breast:
5	chr2:74367938..74377304-chr2:74421816..74428438,25	K562	blood:
6	chr2:74427752..74429271-chr2:74756922..74758791,2	K562	blood:
7	chr2:74153459..74155877-chr2:74426669..74428848,2	K562	blood:
8	chr2:74400907..74407799-chr2:74422654..74428562,23	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115317	Chromatin interaction
ENSG00000114978	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000115307	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000217702	Chromatin interaction
ENSG00000225439	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1095968	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12053233	0.82[GIH][hapmap]
rs12196	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13426653	0.85[EUR][1000 genomes]
rs1620482	0.86[GIH][hapmap]
rs1667601	0.88[CEU][hapmap]
rs1723281	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1723285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4853016	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546893	0.85[EUR][1000 genomes]
rs6546894	0.84[EUR][1000 genomes]
rs702462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7587117	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap]
rs8001	0.84[EUR][1000 genomes]
rs828853	0.84[EUR][1000 genomes]
rs828855	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828856	0.87[EUR][1000 genomes]
rs828857	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828859	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828882	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs828883	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs828884	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs828888	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs828889	0.87[GIH][hapmap]
rs828903	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs844168	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription 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	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS 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	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7340453	MTHFD2	cis	multi-tissue	Pritchard
rs7340453	MTHFD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74425000-74428600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr2:74425000-74428800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:74425200-74428600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:74425200-74428600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:74425400-74428400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr2:74425400-74428600	Active TSS	GM12878-XiMat	blood
7	chr2:74426600-74428600	Flanking Active TSS	Dnd41	blood
8	chr2:74426600-74431600	Weak transcription	Spleen	Spleen
9	chr2:74426800-74429400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:74427000-74428200	Transcr. at gene 5' and 3'	A549	lung
11	chr2:74427000-74428400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:74427000-74429000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:74427000-74429000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:74427000-74429400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:74427200-74428200	Flanking Active TSS	HMEC	breast
16	chr2:74427200-74428400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:74427200-74428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:74427200-74428400	Weak transcription	Stomach Mucosa	stomach
19	chr2:74427200-74428600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:74427200-74429000	Flanking Active TSS	Hela-S3	cervix
21	chr2:74427200-74429200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:74427200-74429600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:74427200-74431400	Weak transcription	Small Intestine	intestine
24	chr2:74427200-74431600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:74427200-74431600	Weak transcription	Colonic Mucosa	Colon
26	chr2:74427200-74432400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:74427200-74432600	Weak transcription	Fetal Intestine Small	intestine
28	chr2:74427200-74433600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:74427200-74433600	Weak transcription	Lung	lung
30	chr2:74427200-74438200	Weak transcription	Fetal Kidney	kidney
31	chr2:74427400-74428200	Weak transcription	Left Ventricle	heart
32	chr2:74427400-74428400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:74427400-74428400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr2:74427400-74428400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:74427400-74428600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr2:74427400-74428600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:74427400-74429000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:74427400-74429200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr2:74427400-74429200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:74427400-74429200	Enhancers	HSMM	muscle
41	chr2:74427400-74429600	Weak transcription	Fetal Stomach	stomach
42	chr2:74427400-74429600	Weak transcription	Fetal Thymus	thymus
43	chr2:74427400-74430000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:74427400-74430600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:74427400-74431400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:74427400-74431600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:74427400-74431600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:74427400-74431600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr2:74427400-74431600	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:74427400-74431600	Weak transcription	Pancreas	Pancrea

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