Variant report

Variant	rs1667627
Chromosome Location	chr2:74429192-74429193
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	MYC	chr2:74428747-74429349	MCF10A-Er-Src	breast:	n/a	n/a
2	E2F4	chr2:74428909-74429434	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:74428553-74429281	U87	brain:	n/a	n/a
4	STAT3	chr2:74428760-74429310	MCF10A-Er-Src	breast:	n/a	chr2:74428941-74428950 chr2:74429166-74429174
5	POLR2A	chr2:74429015-74429363	MCF10A-Er-Src	breast:	n/a	n/a
6	FOSL2	chr2:74428696-74429195	MCF-7	breast:	n/a	chr2:74428941-74428951 chr2:74428941-74428951 chr2:74428942-74428949 chr2:74428942-74428951 chr2:74428940-74428952
7	POLR2A	chr2:74424020-74429252	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:74428559-74429275	U87	brain:	n/a	n/a
9	FOS	chr2:74428732-74429298	MCF10A-Er-Src	breast:	n/a	chr2:74428941-74428951 chr2:74428941-74428951 chr2:74428942-74428949 chr2:74428942-74428951 chr2:74428940-74428952
10	POLR2A	chr2:74428612-74429626	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
2	chr2:74373671..74376054-chr2:74427539..74429224,2	MCF-7	breast:
3	chr2:74427752..74429271-chr2:74756922..74758791,2	K562	blood:
4	chr2:74372510..74375286-chr2:74428494..74430011,2	K562	blood:

Variant related genes	Relation type
MTHFD2	TF binding region
ENSG00000115307	Chromatin interaction
ENSG00000115317	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000225439	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1056528	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1095966	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1095967	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12469365	0.84[EUR][1000 genomes]
rs1667600	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1667610	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108163	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108165	0.84[EUR][1000 genomes]
rs4630794	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs702465	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]
rs828852	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs828860	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828861	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828874	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs828875	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs828887	0.90[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828891	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828893	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844169	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs860455	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs895988	0.82[GIH][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1667627	MTHFD2	cis	multi-tissue	Pritchard
rs1667627	MOBK1B	Cis_1M	lymphoblastoid	RTeQTL
rs1667627	MTHFD2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74426600-74431600	Weak transcription	Spleen	Spleen
2	chr2:74426800-74429400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:74427000-74429400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:74427200-74429200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:74427200-74429600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr2:74427200-74431400	Weak transcription	Small Intestine	intestine
7	chr2:74427200-74431600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:74427200-74431600	Weak transcription	Colonic Mucosa	Colon
9	chr2:74427200-74432400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:74427200-74432600	Weak transcription	Fetal Intestine Small	intestine
11	chr2:74427200-74433600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:74427200-74433600	Weak transcription	Lung	lung
13	chr2:74427200-74438200	Weak transcription	Fetal Kidney	kidney
14	chr2:74427400-74429200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr2:74427400-74429200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:74427400-74429200	Enhancers	HSMM	muscle
17	chr2:74427400-74429600	Weak transcription	Fetal Stomach	stomach
18	chr2:74427400-74429600	Weak transcription	Fetal Thymus	thymus
19	chr2:74427400-74430000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:74427400-74430600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:74427400-74431400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:74427400-74431600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:74427400-74431600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:74427400-74431600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:74427400-74431600	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:74427400-74431600	Weak transcription	Pancreas	Pancrea
27	chr2:74427400-74431600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:74427400-74432200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:74427400-74432400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:74427400-74432800	Weak transcription	Gastric	stomach
31	chr2:74427400-74432800	Weak transcription	Right Atrium	heart
32	chr2:74427400-74432800	Weak transcription	Thymus	Thymus
33	chr2:74427400-74433400	Weak transcription	Esophagus	oesophagus
34	chr2:74427400-74435400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:74427400-74441000	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:74427400-74441200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:74427400-74448400	Weak transcription	Brain Anterior Caudate	brain
38	chr2:74427400-74453000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:74427400-74453200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:74427400-74460200	Weak transcription	Brain Substantia Nigra	brain
41	chr2:74427400-74462000	Weak transcription	Brain Angular Gyrus	brain
42	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
43	chr2:74427600-74429200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:74427600-74429400	Enhancers	NHLF	lung
45	chr2:74427600-74429600	Enhancers	NHDF-Ad	bronchial
46	chr2:74427600-74429600	Enhancers	Osteobl	bone
47	chr2:74427600-74431200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:74427600-74431400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:74427600-74431400	Weak transcription	Aorta	Aorta
50	chr2:74427600-74431400	Weak transcription	Rectal Mucosa Donor 29	rectum

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