Variant report

Variant	rs13090873
Chromosome Location	chr3:112165339-112165340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13090295	0.82[AMR][1000 genomes]
rs1488257	0.87[ASN][1000 genomes]
rs1879515	0.92[ASN][1000 genomes]
rs1961790	0.96[ASN][1000 genomes]
rs2633540	0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2633552	0.91[ASN][1000 genomes]
rs2633553	0.91[ASN][1000 genomes]
rs2633559	0.91[ASN][1000 genomes]
rs2633564	0.87[ASN][1000 genomes]
rs2633565	0.87[ASN][1000 genomes]
rs2633568	0.91[ASN][1000 genomes]
rs2633569	0.91[ASN][1000 genomes]
rs2633586	0.91[ASN][1000 genomes]
rs2633587	0.90[ASN][1000 genomes]
rs2633590	0.91[ASN][1000 genomes]
rs2683910	0.93[ASN][1000 genomes]
rs2683911	0.93[ASN][1000 genomes]
rs2683912	0.92[ASN][1000 genomes]
rs2683914	0.87[ASN][1000 genomes]
rs2683915	0.87[ASN][1000 genomes]
rs2683916	0.91[ASN][1000 genomes]
rs2705511	0.91[ASN][1000 genomes]
rs2705513	0.91[ASN][1000 genomes]
rs2705528	0.90[ASN][1000 genomes]
rs2705545	0.93[ASN][1000 genomes]
rs2952322	0.91[ASN][1000 genomes]
rs3109032	0.91[ASN][1000 genomes]
rs3112270	0.86[ASN][1000 genomes]
rs721361	0.91[ASN][1000 genomes]
rs721362	0.91[ASN][1000 genomes]
rs7625194	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939579	0.93[ASN][1000 genomes]
rs939580	0.93[ASN][1000 genomes]

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	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13090873	ATG3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112161200-112167400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr3:112163000-112166800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:112163800-112166000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:112164000-112165600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:112164000-112166000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:112164000-112168400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:112164200-112165600	Enhancers	HSMM	muscle
8	chr3:112164200-112165800	Enhancers	HSMMtube	muscle
9	chr3:112164600-112165800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:112165000-112165400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:112165000-112165400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:112165000-112165400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:112165000-112165600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:112165000-112165600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:112165000-112166600	Enhancers	Adipose Nuclei	Adipose
16	chr3:112165200-112165400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:112165200-112165600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:112165200-112165600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:112165200-112165600	Enhancers	Primary B cells from cord blood	blood
20	chr3:112165200-112165600	Enhancers	Psoas Muscle	Psoas
21	chr3:112165200-112165600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr3:112165200-112165600	Enhancers	GM12878-XiMat	blood
23	chr3:112165200-112165800	Enhancers	Primary B cells from peripheral blood	blood

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