Variant report

Variant	rs9989009
Chromosome Location	chr12:66458362-66458363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10735933	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878787	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9989009	RP11-745O10.2	cis	Whole Blood	GTEx
rs9989009	IRAK3	Cis_1M	lymphoblastoid	RTeQTL
rs9989009	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66453600-66459000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:66453800-66460800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:66454200-66459600	Weak transcription	Fetal Brain Female	brain
4	chr12:66455800-66461200	Enhancers	NHDF-Ad	bronchial
5	chr12:66456000-66458400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr12:66456000-66458800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:66456000-66458800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:66456000-66459400	Weak transcription	Fetal Lung	lung
9	chr12:66456000-66460200	Weak transcription	Fetal Kidney	kidney
10	chr12:66456200-66458800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr12:66456200-66458800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:66456200-66458800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:66456200-66459600	Weak transcription	HepG2	liver
14	chr12:66456600-66458800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:66457000-66458800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr12:66457200-66460000	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:66457400-66459400	Weak transcription	Fetal Brain Male	brain
18	chr12:66457400-66459800	Weak transcription	Fetal Stomach	stomach
19	chr12:66457800-66459600	Enhancers	Osteobl	bone
20	chr12:66457800-66461200	Enhancers	NHLF	lung
21	chr12:66458000-66458400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:66458000-66458600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:66458200-66458400	Enhancers	Brain Germinal Matrix	brain

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