Variant report

Variant	rs12109828
Chromosome Location	chr5:107976529-107976530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107819554..107821967-chr5:107976343..107978494,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13163102	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13171274	1.00[JPT][hapmap]
rs34304283	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34465355	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34961984	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35153895	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35858291	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36019130	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36052796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36066723	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59214651	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67326538	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67718253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871967	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71592759	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72785503	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72785509	1.00[ASN][1000 genomes]
rs7444560	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7709109	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7731577	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1019409	chr5:107934028-107991426	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12109828	FER	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107970200-107977800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:107970600-107977800	Weak transcription	Osteobl	bone
3	chr5:107972600-107977400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:107972600-107977600	Weak transcription	GM12878-XiMat	blood
5	chr5:107973600-107977400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:107973600-107977400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:107973600-107977800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:107973600-107977800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:107973600-107977800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:107973600-107977800	Weak transcription	HMEC	breast
11	chr5:107973800-107977800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:107974800-107979000	Enhancers	Fetal Heart	heart
13	chr5:107975200-107977400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:107975400-107977400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:107975400-107977800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:107975400-107977800	Weak transcription	NHDF-Ad	bronchial
17	chr5:107975600-107977400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:107975600-107977800	Weak transcription	NHLF	lung
19	chr5:107975800-107977600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:107975800-107977600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:107976400-107977600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:107976400-107977600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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