Variant report

Variant	rs4698747
Chromosome Location	chr4:110600568-110600569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110596739..110598343-chr4:110599981..110601558,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10010159	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10020263	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032323	0.93[ASN][1000 genomes]
rs1008326	0.93[ASN][1000 genomes]
rs1029449	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1029450	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1029451	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1042891	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11098039	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11098040	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11724306	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11931318	0.93[ASN][1000 genomes]
rs12498588	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12504296	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12511995	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12646055	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12647060	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13103167	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13112432	0.84[EUR][1000 genomes]
rs13151303	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2079131	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2107050	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2107051	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2285712	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28380238	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28850086	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28892996	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3181191	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3182325	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34925690	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35838666	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3733611	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3756256	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3796911	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3796912	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4698744	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4698745	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698748	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698776	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698777	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698780	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5030594	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59207576	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6533444	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533445	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6816926	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6825095	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6831930	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6833490	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6834082	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6834701	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6851190	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6851356	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6856535	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs726583	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs726584	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs735642	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs763370	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7672819	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs767598	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7699736	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7699969	0.94[ASN][1000 genomes]
rs9990765	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9993532	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9996648	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9996730	0.85[AMR][1000 genomes];0.87[EUR][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	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
2	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
3	nsv967784	chr4:110594675-110601981	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3408909	chr4:110598728-110601276	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4698747	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

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	chr4:110579200-110608400	Weak transcription	Ovary	ovary
4	chr4:110583600-110605600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:110584200-110606000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:110584400-110608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:110585800-110608800	Weak transcription	Adipose Nuclei	Adipose
8	chr4:110586000-110605200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
10	chr4:110590200-110602600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:110590600-110606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:110591200-110602600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:110591200-110608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:110591600-110605000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:110592000-110611600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:110592800-110603800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:110593000-110601400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:110593000-110608200	Weak transcription	Fetal Lung	lung
19	chr4:110593800-110611600	Weak transcription	K562	blood
20	chr4:110594200-110601800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:110595200-110601400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:110596600-110605600	Weak transcription	GM12878-XiMat	blood
23	chr4:110596800-110601800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:110597000-110601400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr4:110597000-110601600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:110597000-110601600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:110597000-110605800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:110597400-110605600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:110597600-110603600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:110598400-110608200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:110598600-110603600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:110598600-110610400	Weak transcription	HSMMtube	muscle
33	chr4:110598800-110601200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:110598800-110611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:110598800-110622800	Weak transcription	NHEK	skin
36	chr4:110599000-110600800	Weak transcription	Primary T cells from cord blood	blood
37	chr4:110599000-110601400	Weak transcription	Primary B cells from cord blood	blood
38	chr4:110599000-110601400	Weak transcription	Dnd41	blood
39	chr4:110599400-110600600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:110599400-110611400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:110599600-110600800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:110599600-110600800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:110599600-110600800	ZNF genes & repeats	Fetal Thymus	thymus
44	chr4:110599800-110600800	ZNF genes & repeats	Thymus	Thymus
45	chr4:110599800-110601000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr4:110600000-110601600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:110600000-110610600	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:110600000-110611400	Weak transcription	Spleen	Spleen
49	chr4:110600200-110600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:110600200-110600800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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