Variant report

Variant	rs702462
Chromosome Location	chr2:74444431-74444432
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:74439596..74441446-chr2:74442816..74444714,2	MCF-7	breast:
2	chr2:74443809..74445569-chr2:74450000..74451527,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1095968	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12053233	0.82[GIH][hapmap]
rs12196	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426653	0.87[EUR][1000 genomes]
rs1620482	0.86[GIH][hapmap]
rs1667601	0.88[CEU][hapmap]
rs1723281	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1723285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34481365	0.84[AFR][1000 genomes]
rs4853016	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6546893	0.86[EUR][1000 genomes]
rs6546894	0.85[EUR][1000 genomes]
rs7340453	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]
rs7579359	0.84[AFR][1000 genomes]
rs7587117	0.89[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.84[AFR][1000 genomes]
rs8001	0.86[EUR][1000 genomes]
rs828853	0.88[EUR][1000 genomes]
rs828855	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs828856	0.80[EUR][1000 genomes]
rs828857	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828859	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs844168	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv3401140	chr2:74439333-74533696	Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv3380034	chr2:74439354-74533666	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs702462	MTHFD2	cis	multi-tissue	Pritchard
rs702462	MTHFD2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427400-74448400	Weak transcription	Brain Anterior Caudate	brain
2	chr2:74427400-74453000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:74427400-74453200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:74427400-74460200	Weak transcription	Brain Substantia Nigra	brain
5	chr2:74427400-74462000	Weak transcription	Brain Angular Gyrus	brain
6	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
7	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:74428000-74448600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:74428600-74449600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:74429000-74450600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:74429000-74453200	Weak transcription	Ovary	ovary
12	chr2:74429200-74452800	Weak transcription	Fetal Heart	heart
13	chr2:74432600-74444600	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr2:74433600-74447200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:74433600-74447400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:74433600-74447600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:74433600-74447600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:74433600-74448400	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:74433800-74447400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr2:74433800-74447400	Strong transcription	Dnd41	blood
21	chr2:74433800-74447600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:74433800-74447600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:74433800-74448400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:74433800-74449200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:74433800-74449200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:74433800-74449400	Strong transcription	NHEK	skin
27	chr2:74433800-74449600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:74433800-74449800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:74433800-74461800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:74434000-74444800	Strong transcription	Hela-S3	cervix
31	chr2:74434000-74453000	Weak transcription	Psoas Muscle	Psoas
32	chr2:74434200-74447600	Strong transcription	HMEC	breast
33	chr2:74434200-74449400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:74434200-74449800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:74434400-74447600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:74434600-74447600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:74434600-74448800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:74434800-74446800	Strong transcription	HSMM	muscle
39	chr2:74434800-74447200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr2:74434800-74449000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:74434800-74449400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:74434800-74449600	Strong transcription	A549	lung
43	chr2:74435000-74444800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:74435000-74446600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:74435000-74447400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:74435200-74444600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:74435200-74444600	Strong transcription	Fetal Thymus	thymus
48	chr2:74435200-74444600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr2:74435200-74446800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:74435200-74447600	Strong transcription	Left Ventricle	heart

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