Variant report

Variant	rs11098039
Chromosome Location	chr4:110580985-110580986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10010159	0.81[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10017027	0.83[ASN][1000 genomes]
rs10020263	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10032323	0.80[ASN][1000 genomes]
rs1008326	0.80[ASN][1000 genomes]
rs1029449	0.81[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1029450	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1029451	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1042891	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098040	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724306	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11931318	0.80[ASN][1000 genomes]
rs12498588	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12504296	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12504784	0.99[ASN][1000 genomes]
rs12511995	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646055	0.80[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13103167	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13112432	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13151303	0.81[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2079131	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107050	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2107051	0.81[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285712	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28380238	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28850086	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28892996	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181191	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3182325	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34925690	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35838666	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733611	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756256	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796911	0.85[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796912	0.81[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698744	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698745	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4698747	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4698748	0.83[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4698776	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4698777	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4698780	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5030594	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5030606	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59207576	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60916792	0.99[ASN][1000 genomes]
rs6533438	0.81[ASN][1000 genomes]
rs6533444	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533445	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6815377	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6816926	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6825095	0.83[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6831930	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833490	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834082	0.81[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834701	0.81[CEU][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849691	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6851190	0.80[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851356	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6856535	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726583	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726584	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726585	1.00[YRI][hapmap]
rs735642	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763370	0.85[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7672819	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs767598	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7699736	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699969	0.80[ASN][1000 genomes]
rs9990765	0.81[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9993532	0.81[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996648	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996730	0.84[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[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
rs11098039	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 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	chr4:110574200-110581000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:110574200-110583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:110574200-110583200	Weak transcription	Dnd41	blood
9	chr4:110574200-110587400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:110574200-110587600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:110574200-110592600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:110574200-110598400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:110574400-110581400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:110574600-110584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:110574800-110581200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:110574800-110585000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:110576600-110589200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:110576800-110585000	Weak transcription	Primary B cells from cord blood	blood
19	chr4:110577000-110583200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:110577200-110582800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:110577400-110587000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:110579200-110608400	Weak transcription	Ovary	ovary
23	chr4:110579400-110581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:110579400-110582600	Weak transcription	HepG2	liver
25	chr4:110580000-110583800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:110580000-110585000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:110580000-110587600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:110580200-110583200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:110580200-110584400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:110580200-110588200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr4:110580400-110581200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr4:110580400-110583200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:110580400-110583600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:110580400-110586000	Strong transcription	Fetal Thymus	thymus
35	chr4:110580600-110581200	Strong transcription	Primary T cells from cord blood	blood
36	chr4:110580600-110583200	Weak transcription	Colonic Mucosa	Colon
37	chr4:110580600-110585000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr4:110580600-110585400	Strong transcription	Thymus	Thymus
39	chr4:110580800-110581000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr4:110580800-110583600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:110580800-110583600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr4:110580800-110583600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:110580800-110584600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:110580800-110585000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:110580800-110586200	Strong transcription	Primary T cells fromperipheralblood	blood

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