Variant report

Variant	rs7586009
Chromosome Location	chr2:47098968-47098969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47090235..47092918-chr2:47097599..47101021,3	MCF-7	breast:
2	chr2:46635224..46636896-chr2:47097886..47099618,2	K562	blood:
3	chr2:47090932..47093408-chr2:47096445..47099891,3	K562	blood:
4	chr2:47098032..47101005-chr2:47166387..47169374,2	K562	blood:
5	chr2:47087833..47089344-chr2:47097386..47099191,2	MCF-7	breast:
6	chr2:47091177..47094224-chr2:47098051..47100562,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11125098	1.00[JPT][hapmap]
rs13415138	0.94[JPT][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	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
rs7586009	MCFD2	cis	cerebellum	SCAN
rs7586009	MCFD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47080800-47103600	Enhancers	Placenta	Placenta
2	chr2:47094000-47100600	Weak transcription	Fetal Intestine Small	intestine
3	chr2:47094000-47104200	Weak transcription	Gastric	stomach
4	chr2:47094200-47100200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:47094200-47100400	Weak transcription	Colonic Mucosa	Colon
6	chr2:47094200-47100400	Weak transcription	Small Intestine	intestine
7	chr2:47094400-47101000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:47094600-47100200	Weak transcription	Ovary	ovary
9	chr2:47095200-47100000	Weak transcription	HUVEC	blood vessel
10	chr2:47095200-47100600	Weak transcription	Stomach Mucosa	stomach
11	chr2:47095200-47100800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:47095200-47104200	Weak transcription	Pancreas	Pancrea
13	chr2:47095600-47100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:47095800-47100200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:47095800-47100200	Weak transcription	NHEK	skin
16	chr2:47096000-47099600	Enhancers	Fetal Muscle Trunk	muscle
17	chr2:47096200-47100600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:47096200-47103200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:47096200-47105000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:47096400-47099400	Enhancers	Fetal Muscle Leg	muscle
21	chr2:47096600-47106400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:47096800-47100800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:47097000-47100000	Weak transcription	Spleen	Spleen
24	chr2:47097000-47100200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:47097000-47100200	Weak transcription	HMEC	breast
26	chr2:47097200-47100400	Weak transcription	Fetal Heart	heart
27	chr2:47097200-47100800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:47097400-47116200	Enhancers	NHDF-Ad	bronchial
29	chr2:47097600-47099000	Weak transcription	A549	lung
30	chr2:47097600-47099200	Weak transcription	Fetal Lung	lung
31	chr2:47097600-47100000	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:47097800-47099000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:47097800-47099400	Weak transcription	Right Atrium	heart
34	chr2:47097800-47099400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:47097800-47099600	Weak transcription	NHLF	lung
36	chr2:47097800-47100000	Weak transcription	NH-A	brain
37	chr2:47097800-47100400	Weak transcription	Left Ventricle	heart
38	chr2:47097800-47101000	Weak transcription	Esophagus	oesophagus
39	chr2:47098000-47099000	Weak transcription	Right Ventricle	heart
40	chr2:47098000-47099400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:47098000-47099800	Weak transcription	Fetal Stomach	stomach
42	chr2:47098000-47100000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:47098200-47099600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:47098200-47100000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:47098200-47100000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:47098200-47100000	Weak transcription	HSMM	muscle
47	chr2:47098200-47100200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:47098200-47100400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:47098200-47100400	Weak transcription	Lung	lung
50	chr2:47098200-47101800	Enhancers	K562	blood

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