Variant report

Variant	rs11724306
Chromosome Location	chr4:110583165-110583166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110568027..110570287-chr4:110582225..110584531,2	K562	blood:
2	chr4:110582260..110584595-chr4:110587879..110590432,2	K562	blood:
3	chr4:110582184..110585367-chr4:110588932..110592046,3	K562	blood:
4	chr4:110370787..110372375-chr4:110582316..110584517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243227	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10010159	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10017027	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10020263	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1029449	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1029450	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1029451	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1042891	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098039	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098040	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12498588	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504296	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12504784	0.97[ASN][1000 genomes]
rs12511995	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646055	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12647060	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103167	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112432	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13151303	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079131	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2107050	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2107051	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285712	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28380238	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28850086	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28892996	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181191	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3182325	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34925690	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35838666	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733611	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756256	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796911	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796912	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698744	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698745	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4698747	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4698748	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4698776	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4698777	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4698780	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030594	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5030606	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59207576	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60916792	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6533444	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533445	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815377	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6816926	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6825095	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831930	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6833490	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6834082	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834701	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849691	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6851190	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6851356	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6856535	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726583	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726584	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs735642	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs763370	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672819	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767598	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7699736	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9990765	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9993532	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996648	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996730	0.95[AMR][1000 genomes];0.98[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11724306	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110571000-110605400	Weak transcription	Left Ventricle	heart
2	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
3	chr4:110573200-110588200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:110574000-110586600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:110574200-110583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:110574200-110583200	Weak transcription	Dnd41	blood
7	chr4:110574200-110587400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:110574200-110587600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:110574200-110592600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:110574200-110598400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:110574600-110584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:110574800-110585000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:110576600-110589200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:110576800-110585000	Weak transcription	Primary B cells from cord blood	blood
15	chr4:110577000-110583200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:110577400-110587000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:110579200-110608400	Weak transcription	Ovary	ovary
18	chr4:110580000-110583800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:110580000-110585000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:110580000-110587600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:110580200-110583200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:110580200-110584400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:110580200-110588200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:110580400-110583200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:110580400-110583600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:110580400-110586000	Strong transcription	Fetal Thymus	thymus
27	chr4:110580600-110583200	Weak transcription	Colonic Mucosa	Colon
28	chr4:110580600-110585000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:110580600-110585400	Strong transcription	Thymus	Thymus
30	chr4:110580800-110583600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:110580800-110583600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr4:110580800-110583600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:110580800-110584600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:110580800-110585000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr4:110580800-110586200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:110581000-110586200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr4:110581200-110583600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:110581200-110584200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:110581200-110587000	Weak transcription	Placenta	Placenta
40	chr4:110581400-110587800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:110581600-110583400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr4:110581600-110596800	Weak transcription	Lung	lung
43	chr4:110582800-110586000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:110582800-110586200	Enhancers	Brain Germinal Matrix	brain
45	chr4:110583000-110584200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:110583000-110585800	Strong transcription	Primary T cells from cord blood	blood
47	chr4:110583000-110587000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:110583000-110587800	Enhancers	Fetal Brain Male	brain
49	chr4:110583000-110596600	Weak transcription	HepG2	liver

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