Variant report

Variant	rs1447614
Chromosome Location	chr3:160603241-160603242
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12636616	0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12638359	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12638531	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1447611	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1447625	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1447627	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34673399	0.97[ASN][1000 genomes]
rs56707676	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61344153	0.97[ASN][1000 genomes]
rs61651193	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6785317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6800633	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6806892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7636214	1.00[ASN][1000 genomes]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3391648	chr3:160602299-160620598	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1447614	FOXG1	trans	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160596400-160603800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:160598000-160603400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:160602200-160604600	Enhancers	Fetal Thymus	thymus
4	chr3:160602200-160604600	Enhancers	Thymus	Thymus
5	chr3:160602800-160603400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:160602800-160604400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:160602800-160604400	Enhancers	Brain Angular Gyrus	brain
8	chr3:160603000-160603400	Enhancers	Brain Hippocampus Middle	brain
9	chr3:160603000-160604000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:160603000-160604400	Enhancers	Psoas Muscle	Psoas
11	chr3:160603200-160603400	Enhancers	Brain Cingulate Gyrus	brain
12	chr3:160603200-160603400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:160603200-160603400	Enhancers	Fetal Muscle Trunk	muscle
14	chr3:160603200-160603600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:160603200-160603600	ZNF genes & repeats	Esophagus	oesophagus
16	chr3:160603200-160603600	Enhancers	Fetal Stomach	stomach
17	chr3:160603200-160603600	Enhancers	Right Atrium	heart
18	chr3:160603200-160603600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr3:160603200-160603800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:160603200-160603800	Enhancers	GM12878-XiMat	blood
21	chr3:160603200-160604000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:160603200-160604000	Flanking Active TSS	Dnd41	blood
23	chr3:160603200-160604200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:160603200-160604200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:160603200-160604200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr3:160603200-160604200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:160603200-160604200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:160603200-160604200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:160603200-160604200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr3:160603200-160604400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:160603200-160604400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:160603200-160604400	Enhancers	Adipose Nuclei	Adipose
33	chr3:160603200-160604400	Enhancers	Duodenum Mucosa	Duodenum
34	chr3:160603200-160604400	Enhancers	Left Ventricle	heart
35	chr3:160603200-160604600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:160603200-160604600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr3:160603200-160604600	Enhancers	Fetal Muscle Leg	muscle
38	chr3:160603200-160604600	Enhancers	Placenta	Placenta

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