Variant report

Variant	rs331147
Chromosome Location	chr3:78917012-78917013
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11127635	0.90[CEU][hapmap]
rs17016554	0.81[CEU][hapmap]
rs182796	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331141	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs331142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331144	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331146	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3856695	0.90[CEU][hapmap]
rs6770639	0.85[CEU][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877020	chr3:78913203-78975982	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs331147	FGF10	trans	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78907600-78920200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:78913200-78918600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:78916000-78917200	Enhancers	Brain Angular Gyrus	brain
4	chr3:78916000-78918000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:78916200-78917400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:78916200-78917400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:78916200-78917400	Enhancers	Brain Hippocampus Middle	brain
8	chr3:78916200-78917400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:78916200-78917400	Enhancers	Fetal Kidney	kidney
10	chr3:78916200-78918000	Enhancers	Osteobl	bone
11	chr3:78916200-78923000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:78916400-78917400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:78916400-78917400	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr3:78916400-78918000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:78916400-78918000	Enhancers	Hela-S3	cervix
16	chr3:78916400-78918000	Enhancers	NHDF-Ad	bronchial
17	chr3:78916400-78921400	Enhancers	HepG2	liver
18	chr3:78916600-78917200	Active TSS	Brain Substantia Nigra	brain
19	chr3:78916600-78917400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:78916600-78917400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:78916600-78917400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:78916600-78918000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr3:78916600-78918000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:78916600-78918800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:78916800-78917400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:78916800-78917400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:78916800-78917400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:78916800-78918000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr3:78916800-78918200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:78916800-78919000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr3:78916800-78919400	Weak transcription	Brain Anterior Caudate	brain
32	chr3:78917000-78917400	Enhancers	Fetal Brain Male	brain
33	chr3:78917000-78917400	Enhancers	A549	lung
34	chr3:78917000-78917600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:78917000-78917600	Enhancers	NH-A	brain
36	chr3:78917000-78918000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:78917000-78918000	Enhancers	Brain Germinal Matrix	brain
38	chr3:78917000-78918000	Enhancers	Fetal Lung	lung
39	chr3:78917000-78918400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:78917000-78920000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:78917000-78921000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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