Variant report

Variant	rs13093350
Chromosome Location	chr3:112993063-112993064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13094203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291905	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2650100	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34239722	0.85[EUR][1000 genomes]
rs35341359	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271355	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56163361	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66518523	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808951	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh 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
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13093350	BOC	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
3	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
4	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:112982800-112993600	Weak transcription	HMEC	breast
7	chr3:112983800-112995000	Weak transcription	Lung	lung
8	chr3:112984000-112994400	Weak transcription	HSMMtube	muscle
9	chr3:112984200-112993600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:112984200-112994400	Weak transcription	HSMM	muscle
11	chr3:112984600-112993400	Weak transcription	Fetal Brain Male	brain
12	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:112985400-112993600	Strong transcription	Fetal Lung	lung
15	chr3:112986200-112994200	Strong transcription	Ovary	ovary
16	chr3:112986400-112994600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:112986600-112993800	Weak transcription	Brain Substantia Nigra	brain
18	chr3:112987200-112993400	Strong transcription	Fetal Stomach	stomach
19	chr3:112987200-112994400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
21	chr3:112988000-112993600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:112988000-112993800	Weak transcription	Brain Angular Gyrus	brain
23	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr3:112988200-112993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:112988200-112993600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:112988200-112993800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:112988200-112994200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:112988200-112994200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:112988200-112994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:112988400-112994000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:112988400-112994600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
33	chr3:112989000-112993600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:112989000-112994000	Weak transcription	Brain Anterior Caudate	brain
35	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:112989200-112993600	Strong transcription	Rectal Smooth Muscle	rectum
37	chr3:112989400-112993800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:112989400-112993800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:112989400-112994200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:112989600-112994200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:112989800-112993400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:112989800-112994400	Weak transcription	NH-A	brain
43	chr3:112990200-112994800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:112990400-112993800	Strong transcription	Colon Smooth Muscle	Colon
45	chr3:112990400-112994600	Strong transcription	Esophagus	oesophagus
46	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:112990600-112994000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:112990600-113004000	Weak transcription	NHEK	skin
49	chr3:112990800-112993800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:112990800-112994000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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