Variant report

Variant	rs13112432
Chromosome Location	chr4:110581987-110581988
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110581396..110582917-chr4:110583378..110586264,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10010159	0.86[ASN][1000 genomes]
rs1029449	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1029450	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1029451	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1042891	0.86[ASN][1000 genomes]
rs11098039	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098040	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11724306	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12498588	0.86[ASN][1000 genomes]
rs12504296	0.84[EUR][1000 genomes]
rs12504784	0.85[ASN][1000 genomes]
rs12511995	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12646055	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12647060	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13103167	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13151303	0.86[ASN][1000 genomes]
rs2079131	0.85[ASN][1000 genomes]
rs2107050	0.85[EUR][1000 genomes]
rs2107051	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28380238	0.85[ASN][1000 genomes]
rs28850086	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28892996	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3181191	0.86[ASN][1000 genomes]
rs34925690	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35838666	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733611	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3756256	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796911	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3796912	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4698744	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4698747	0.84[EUR][1000 genomes]
rs4698748	0.81[AMR][1000 genomes]
rs4698776	0.85[EUR][1000 genomes]
rs4698780	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5030606	0.85[ASN][1000 genomes]
rs59207576	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60916792	0.85[ASN][1000 genomes]
rs6533444	0.86[ASN][1000 genomes]
rs6533445	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6816926	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6825095	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6831930	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6833490	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6834082	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6834701	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6851190	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6851356	0.84[ASN][1000 genomes]
rs6856535	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs726583	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs726584	0.86[ASN][1000 genomes]
rs735642	0.85[ASN][1000 genomes]
rs763370	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7672819	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7699736	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9990765	0.86[ASN][1000 genomes]
rs9993532	0.86[ASN][1000 genomes]
rs9996648	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9996730	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv508303	chr4:110579305-110604452	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2175637	chr4:110581987-110581988	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13112432	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110570400-110582000	Weak transcription	HSMM	muscle
2	chr4:110571000-110605400	Weak transcription	Left Ventricle	heart
3	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
4	chr4:110573200-110588200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:110574000-110586600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:110574200-110583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:110574200-110583200	Weak transcription	Dnd41	blood
8	chr4:110574200-110587400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:110574200-110587600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:110574200-110592600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:110574200-110598400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:110574600-110584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:110574800-110585000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:110576600-110589200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:110576800-110585000	Weak transcription	Primary B cells from cord blood	blood
16	chr4:110577000-110583200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:110577200-110582800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:110577400-110587000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:110579200-110608400	Weak transcription	Ovary	ovary
20	chr4:110579400-110582600	Weak transcription	HepG2	liver
21	chr4:110580000-110583800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:110580000-110585000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:110580000-110587600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:110580200-110583200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:110580200-110584400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:110580200-110588200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:110580400-110583200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:110580400-110583600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:110580400-110586000	Strong transcription	Fetal Thymus	thymus
30	chr4:110580600-110583200	Weak transcription	Colonic Mucosa	Colon
31	chr4:110580600-110585000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:110580600-110585400	Strong transcription	Thymus	Thymus
33	chr4:110580800-110583600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:110580800-110583600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:110580800-110583600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:110580800-110584600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr4:110580800-110585000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:110580800-110586200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr4:110581000-110583000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:110581000-110586200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr4:110581200-110583000	Weak transcription	Primary T cells from cord blood	blood
42	chr4:110581200-110583600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:110581200-110584200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:110581200-110587000	Weak transcription	Placenta	Placenta
45	chr4:110581400-110587800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:110581600-110583400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:110581600-110596800	Weak transcription	Lung	lung

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