Variant report

Variant	rs56117810
Chromosome Location	chr12:62656247-62656248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr12:62656117-62656477	K562	blood:	n/a	n/a
2	FOXA1	chr12:62656008-62656347	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:62655605..62659464-chr12:62666404..62669367,3	MCF-7	breast:
2	chr12:62654217..62657046-chr12:62663377..62665322,2	MCF-7	breast:
3	chr12:62652133..62655871-chr12:62655983..62662487,11	MCF-7	breast:
4	chr12:62655349..62657047-chr12:62679451..62682402,2	K562	blood:

Variant related genes	Relation type
FAM19A2	TF binding region
ENSG00000135655	Chromatin interaction
ENSG00000198673	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1074956	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074957	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610579	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612349	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612366	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613953	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11614866	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614922	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615398	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615693	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586916	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17659468	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17659736	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17659938	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17660079	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17660575	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17661264	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17716130	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17716446	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17716876	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17716977	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17717132	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17717265	1.00[ASN][1000 genomes]
rs17717700	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35496480	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635136	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642112	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55718649	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55905969	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55938311	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56049136	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56059115	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104969	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56126088	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181846	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277058	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56291672	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56298756	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56309606	0.84[EUR][1000 genomes]
rs56402690	0.84[EUR][1000 genomes]
rs7133047	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296326	0.84[EUR][1000 genomes]
rs73135231	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135240	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135251	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135253	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135257	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135269	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135271	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135272	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135273	0.85[AMR][1000 genomes]
rs73135275	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135280	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135290	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135294	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135297	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135299	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136829	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136830	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136831	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136834	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136848	1.00[ASN][1000 genomes]
rs73136851	0.82[EUR][1000 genomes]
rs73136856	0.82[EUR][1000 genomes]
rs73136858	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136860	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136862	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136863	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136864	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136866	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136869	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136870	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137504	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137512	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137519	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137521	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137525	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137528	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139022	1.00[ASN][1000 genomes]
rs7316131	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970028	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970042	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7970114	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970298	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035150	chr12:62615347-62785005	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56117810	USP15	cis	Artery Aorta	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62652200-62657600	Active TSS	GM12878-XiMat	blood
2	chr12:62652400-62656600	Active TSS	K562	blood
3	chr12:62653000-62656600	Active TSS	NHLF	lung
4	chr12:62653200-62656400	Active TSS	NHDF-Ad	bronchial
5	chr12:62654600-62656600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:62654800-62656800	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr12:62654800-62660600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:62655000-62656400	Flanking Active TSS	Dnd41	blood
9	chr12:62655000-62657400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr12:62655000-62657600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:62655000-62657800	Weak transcription	Gastric	stomach
12	chr12:62655000-62659400	Weak transcription	Esophagus	oesophagus
13	chr12:62655000-62663400	Weak transcription	Lung	lung
14	chr12:62655200-62656400	Flanking Active TSS	Liver	Liver
15	chr12:62655200-62656400	Active TSS	HepG2	liver
16	chr12:62655200-62657200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr12:62655200-62657600	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr12:62655200-62658400	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr12:62655400-62656400	Enhancers	Brain Anterior Caudate	brain
20	chr12:62655400-62656400	Enhancers	Fetal Kidney	kidney
21	chr12:62655400-62656600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:62655400-62656600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr12:62655400-62656600	Enhancers	Rectal Smooth Muscle	rectum
24	chr12:62655400-62656800	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:62655400-62657800	Enhancers	Fetal Brain Male	brain
26	chr12:62655400-62658200	Enhancers	Colon Smooth Muscle	Colon
27	chr12:62655400-62660800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:62655400-62685600	Weak transcription	HSMM	muscle
29	chr12:62655600-62656600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr12:62655600-62656600	Enhancers	Fetal Intestine Large	intestine
31	chr12:62655600-62656600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr12:62655600-62656600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:62655600-62656800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr12:62655600-62656800	Enhancers	Brain Hippocampus Middle	brain
35	chr12:62655600-62661400	Weak transcription	NH-A	brain
36	chr12:62655800-62656400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr12:62655800-62656400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:62655800-62656400	Enhancers	A549	lung
39	chr12:62655800-62656600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:62655800-62656600	Enhancers	Aorta	Aorta
41	chr12:62655800-62656600	Enhancers	Fetal Brain Female	brain
42	chr12:62655800-62656600	Enhancers	Left Ventricle	heart
43	chr12:62655800-62656600	Enhancers	Ovary	ovary
44	chr12:62655800-62656600	Enhancers	HMEC	breast
45	chr12:62655800-62656600	Enhancers	HUVEC	blood vessel
46	chr12:62655800-62657000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr12:62655800-62657200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:62655800-62657200	Enhancers	NHEK	skin
49	chr12:62655800-62657400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr12:62655800-62658400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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