Variant report

Variant	rs13415138
Chromosome Location	chr2:47081551-47081552
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	MAX	chr2:47081386-47084203	A549	lung:	n/a	chr2:47083633-47083643 chr2:47083889-47083899 chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082693-47082703 chr2:47082538-47082547
2	EP300	chr2:47081547-47083239	SK-N-SH	brain:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082262-47082276 chr2:47082538-47082547

Variant related genes	Relation type
ENSG00000226548	TF binding region
LINC01119	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11125098	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13422107	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2278712	0.84[EUR][1000 genomes]
rs34392693	0.85[EUR][1000 genomes]
rs4953431	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs4953434	0.85[CEU][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes]
rs58086358	0.84[EUR][1000 genomes]
rs61507430	0.92[EUR][1000 genomes]
rs61542554	0.86[AMR][1000 genomes]
rs72804479	0.84[AMR][1000 genomes]
rs7586009	0.94[JPT][hapmap]
rs9789584	0.91[EUR][1000 genomes]

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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13415138	MCFD2	cis	parietal	SCAN
rs13415138	MCFD2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47069400-47082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:47075200-47084400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:47076600-47081600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:47076800-47081600	Weak transcription	Brain Anterior Caudate	brain
5	chr2:47077200-47086200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:47077400-47081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:47077600-47081600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:47077600-47081600	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:47077600-47081600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:47078000-47081600	Weak transcription	Esophagus	oesophagus
11	chr2:47078000-47082000	Weak transcription	Small Intestine	intestine
12	chr2:47078000-47083400	Weak transcription	Fetal Intestine Large	intestine
13	chr2:47078000-47085200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:47078000-47085200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:47078200-47081600	Weak transcription	Fetal Lung	lung
16	chr2:47078200-47081600	Weak transcription	Spleen	Spleen
17	chr2:47078400-47081600	Weak transcription	Colonic Mucosa	Colon
18	chr2:47078400-47081600	Weak transcription	Fetal Heart	heart
19	chr2:47078400-47081600	Weak transcription	Lung	lung
20	chr2:47078400-47081600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:47078400-47081600	Weak transcription	Right Ventricle	heart
22	chr2:47078400-47083200	Weak transcription	Psoas Muscle	Psoas
23	chr2:47078600-47081600	Weak transcription	Aorta	Aorta
24	chr2:47078600-47081600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:47078600-47081600	Weak transcription	Ovary	ovary
26	chr2:47078600-47081600	Weak transcription	Right Atrium	heart
27	chr2:47078600-47081600	Weak transcription	HSMM	muscle
28	chr2:47078600-47082000	Weak transcription	Stomach Mucosa	stomach
29	chr2:47078600-47082600	Weak transcription	Pancreas	Pancrea
30	chr2:47079200-47082600	Enhancers	HUVEC	blood vessel
31	chr2:47079600-47081600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:47080200-47081600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:47080200-47081600	Weak transcription	Osteobl	bone
34	chr2:47080400-47081600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:47080600-47085000	Weak transcription	K562	blood
36	chr2:47080800-47081600	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:47080800-47084200	Enhancers	Left Ventricle	heart
38	chr2:47080800-47103600	Enhancers	Placenta	Placenta
39	chr2:47081000-47082200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:47081200-47081800	ZNF genes & repeats	A549	lung
41	chr2:47081200-47082200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:47081200-47082800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:47081200-47083800	Enhancers	Rectal Smooth Muscle	rectum
44	chr2:47081200-47087200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:47081400-47081600	Enhancers	Hela-S3	cervix
46	chr2:47081400-47082200	Enhancers	NHEK	skin
47	chr2:47081400-47082600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:47081400-47082600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:47081400-47083000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:47081400-47083000	Enhancers	Adipose Nuclei	Adipose

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