Variant report

Variant	rs702465
Chromosome Location	chr2:74369151-74369152
allele	A/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
2	chr2:74367938..74377304-chr2:74421816..74428438,25	K562	blood:
3	chr2:74366787..74371323-chr2:74423574..74427376,7	MCF-7	breast:
4	chr2:74364840..74367040-chr2:74367594..74369690,3	MCF-7	breast:
5	chr2:74347508..74349291-chr2:74367308..74370110,2	K562	blood:
6	chr2:74356810..74359552-chr2:74365465..74371208,7	MCF-7	breast:
7	chr2:74367123..74369232-chr2:74374914..74376583,2	MCF-7	breast:
8	chr2:74210394..74212955-chr2:74366832..74369511,2	K562	blood:
9	chr2:74345925..74350118-chr2:74367023..74371456,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163170	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1056528	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1095966	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1095967	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667600	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667610	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1667627	0.90[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108163	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4630794	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828852	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828860	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828861	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs828875	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828887	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828891	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828893	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs844169	0.81[EUR][1000 genomes]
rs860455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs895988	0.83[MEX][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	nsv525117	chr2:74358901-74374641	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs702465	MTHFD2	cis	multi-tissue	Pritchard
rs702465	MTHFD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74354400-74373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:74355200-74373800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:74357600-74373800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:74357800-74373600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:74358200-74373800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:74358800-74373800	Weak transcription	HUVEC	blood vessel
7	chr2:74359200-74373600	Weak transcription	Fetal Heart	heart
8	chr2:74359400-74373600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:74359600-74373400	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:74359600-74373800	Weak transcription	Small Intestine	intestine
11	chr2:74359800-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:74359800-74373600	Weak transcription	NH-A	brain
13	chr2:74360000-74369800	Weak transcription	Colonic Mucosa	Colon
14	chr2:74360200-74373600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:74360600-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:74360800-74373600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:74360800-74373800	Weak transcription	Placenta	Placenta
18	chr2:74360800-74374000	Weak transcription	HSMMtube	muscle
19	chr2:74362000-74371600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:74362000-74373600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:74362200-74369200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:74362200-74371400	Weak transcription	Brain Substantia Nigra	brain
23	chr2:74362200-74373400	Weak transcription	Fetal Lung	lung
24	chr2:74362200-74373600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:74362200-74373600	Weak transcription	HMEC	breast
26	chr2:74362200-74374000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:74362200-74374600	Weak transcription	Aorta	Aorta
28	chr2:74362400-74369200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:74362400-74373400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:74362400-74373400	Weak transcription	Right Ventricle	heart
31	chr2:74362400-74373600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:74362400-74373600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:74362400-74373600	Weak transcription	Brain Angular Gyrus	brain
34	chr2:74362400-74373600	Weak transcription	Psoas Muscle	Psoas
35	chr2:74362400-74373800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:74362600-74371400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:74362600-74373400	Weak transcription	Hela-S3	cervix
38	chr2:74362800-74369600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:74362800-74373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:74362800-74373600	Weak transcription	Liver	Liver
41	chr2:74364000-74369800	Strong transcription	HepG2	liver
42	chr2:74364200-74371000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:74364200-74373600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:74364400-74370600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:74364400-74372400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:74364800-74370200	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:74364800-74372000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:74365000-74373400	Strong transcription	Fetal Stomach	stomach
49	chr2:74365200-74372200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:74365200-74372200	Strong transcription	Fetal Muscle Leg	muscle

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