Variant report

Variant	rs6546896
Chromosome Location	chr2:74480602-74480603
allele	C/T
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	CEBPB	chr2:74480501-74480710	HepG2	liver:	n/a	chr2:74480594-74480605 chr2:74480594-74480607

No.	Distal block	Cell Line	Cell type
1	chr2:74480267..74484061-chr2:74484268..74488545,6	K562	blood:
2	chr2:74480267..74481888-chr2:74486741..74488545,2	K562	blood:
3	chr2:74478235..74480981-chr2:74481514..74484984,3	MCF-7	breast:
4	chr2:74469853..74472729-chr2:74479366..74481244,2	MCF-7	breast:
5	chr2:74474393..74476736-chr2:74479092..74481052,2	K562	blood:

Variant related genes	Relation type
SLC4A5	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13024188	0.96[EUR][1000 genomes]
rs2034454	0.91[JPT][hapmap]
rs6731545	0.91[EUR][1000 genomes]
rs7558047	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7561242	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7571842	0.91[JPT][hapmap]
rs895987	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs895988	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv2757807	chr2:74479924-74762425	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	esv2759061	chr2:74479924-74762425	Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6546896	MTHFD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74427400-74484400	Weak transcription	Fetal Lung	lung
2	chr2:74427800-74494200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:74439800-74525200	Weak transcription	Fetal Brain Male	brain
4	chr2:74441800-74490400	Weak transcription	Fetal Brain Female	brain
5	chr2:74444800-74494200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:74448800-74494000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:74449200-74502200	Weak transcription	Spleen	Spleen
8	chr2:74449400-74494000	Weak transcription	Primary T cells from cord blood	blood
9	chr2:74449400-74507000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:74450000-74494000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:74454200-74508200	Weak transcription	Ovary	ovary
12	chr2:74458600-74483400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:74458800-74488200	Weak transcription	Pancreas	Pancrea
14	chr2:74462200-74494000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:74462400-74493800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:74462600-74509600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:74463000-74544800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:74466400-74492800	Weak transcription	Adipose Nuclei	Adipose
19	chr2:74469400-74485200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:74470400-74527800	Weak transcription	Aorta	Aorta
21	chr2:74470400-74528000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:74470600-74481400	Weak transcription	Left Ventricle	heart
23	chr2:74470600-74511800	Weak transcription	Right Ventricle	heart
24	chr2:74470600-74518200	Weak transcription	Gastric	stomach
25	chr2:74473800-74491000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:74473800-74494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:74474000-74494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:74474200-74481200	Weak transcription	Lung	lung
29	chr2:74474200-74495600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:74474400-74481400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:74474400-74528400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:74474600-74481200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:74474600-74540400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:74475800-74481200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:74477000-74489600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:74477000-74494600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:74477600-74493800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:74477800-74482000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:74477800-74483200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:74477800-74490600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:74477800-74494200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:74477800-74494200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:74477800-74494400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:74478400-74482800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:74478400-74488000	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:74479000-74482200	Strong transcription	Brain Hippocampus Middle	brain
47	chr2:74480000-74481200	Weak transcription	Fetal Stomach	stomach
48	chr2:74480000-74481600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:74480000-74481800	Enhancers	Fetal Muscle Leg	muscle
50	chr2:74480000-74494400	Weak transcription	Thymus	Thymus

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