Variant report

Variant	rs12186215
Chromosome Location	chr4:53983710-53983711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17702812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2053650	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4864446	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62324997	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62338967	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62338969	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62338970	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62338994	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62339002	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62339004	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12186215	SCFD2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53965800-53986000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:53968400-53984600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
4	chr4:53980000-53985400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:53980000-53985800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:53980000-53985800	Weak transcription	NHLF	lung
7	chr4:53980000-53986800	Weak transcription	Aorta	Aorta
8	chr4:53980400-53985800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:53980400-53993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:53980800-53985600	Weak transcription	NHDF-Ad	bronchial
11	chr4:53981200-53985800	Weak transcription	Fetal Lung	lung
12	chr4:53981800-53985600	Weak transcription	Fetal Intestine Small	intestine
13	chr4:53981800-53986000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:53982200-53989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:53982600-53983800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:53982600-53983800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:53982600-53984000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:53982600-53984000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr4:53982800-53983800	Enhancers	HMEC	breast
20	chr4:53983200-53983800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:53983200-53983800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:53983200-53983800	Enhancers	Fetal Intestine Large	intestine
23	chr4:53983200-53987400	Weak transcription	Ovary	ovary
24	chr4:53983400-53983800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:53983600-53983800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:53983600-53985000	Weak transcription	Stomach Mucosa	stomach
27	chr4:53983600-53985600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:53983600-53985600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:53983600-53985600	Weak transcription	Osteobl	bone
30	chr4:53983600-53985800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:53983600-53985800	Weak transcription	HSMMtube	muscle
32	chr4:53983600-53985800	Weak transcription	NHEK	skin

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