Variant report

Variant	rs1579862
Chromosome Location	chr2:47070827-47070828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12463795	0.96[YRI][hapmap]
rs12614366	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1579863	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17774133	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs1867821	0.84[CEU][hapmap]
rs1947109	0.85[EUR][1000 genomes]
rs6544930	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs6544931	0.94[ASW][hapmap];0.98[GIH][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs6719049	0.96[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs7597025	0.89[ASW][hapmap];0.98[GIH][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv817840	chr2:47044218-47070827	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1579862	MCFD2	cis	cerebellum	SCAN
rs1579862	MCFD2	cis	parietal	SCAN
rs1579862	LOC388946	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47063400-47072200	Weak transcription	Placenta	Placenta
2	chr2:47063800-47072000	Weak transcription	Lung	lung
3	chr2:47063800-47072200	Weak transcription	Left Ventricle	heart
4	chr2:47063800-47072200	Weak transcription	Pancreas	Pancrea
5	chr2:47063800-47072800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:47063800-47073000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:47064000-47072800	Weak transcription	Right Atrium	heart
8	chr2:47064000-47072800	Weak transcription	Spleen	Spleen
9	chr2:47064000-47073200	Weak transcription	NHLF	lung
10	chr2:47067400-47073400	Weak transcription	Osteobl	bone
11	chr2:47069200-47072800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:47069400-47072800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:47069400-47073000	Weak transcription	Adipose Nuclei	Adipose
14	chr2:47069400-47073400	Weak transcription	Stomach Mucosa	stomach
15	chr2:47069400-47073600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:47069400-47082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:47070200-47072000	Weak transcription	Right Ventricle	heart
18	chr2:47070200-47073200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:47070200-47073800	Enhancers	Stomach Smooth Muscle	stomach
20	chr2:47070400-47073800	Enhancers	Colon Smooth Muscle	Colon
21	chr2:47070800-47072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:47070800-47072800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:47070800-47072800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:47070800-47072800	Weak transcription	NHDF-Ad	bronchial
25	chr2:47070800-47073000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:47070800-47073600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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