Variant report

Variant	rs12513113
Chromosome Location	chr4:110608261-110608262
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	chr4:110608213..110611380-chr4:110623031..110625861,3	K562	blood:
2	chr4:110603636..110605743-chr4:110606577..110610223,4	K562	blood:

Variant related genes	Relation type
ENSG00000138794	Chromatin interaction
ENSG00000005059	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1008327	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13128388	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13846	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1543812	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2158204	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346835	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4698770	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4698775	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62326058	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62327660	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533442	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6533446	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6824270	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6824542	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857252	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6858416	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72674829	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7658262	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7690921	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12513113	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
2	chr4:110579200-110608400	Weak transcription	Ovary	ovary
3	chr4:110584400-110608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:110585800-110608800	Weak transcription	Adipose Nuclei	Adipose
5	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
6	chr4:110591200-110608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:110592000-110611600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:110593800-110611600	Weak transcription	K562	blood
9	chr4:110598600-110610400	Weak transcription	HSMMtube	muscle
10	chr4:110598800-110611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:110598800-110622800	Weak transcription	NHEK	skin
12	chr4:110599400-110611400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:110600000-110610600	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:110600000-110611400	Weak transcription	Spleen	Spleen
15	chr4:110600200-110613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:110600400-110610000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:110600400-110610200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:110600400-110611800	Weak transcription	NHDF-Ad	bronchial
19	chr4:110600600-110611200	Weak transcription	HSMM	muscle
20	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:110601000-110608400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:110601200-110610200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:110601200-110611400	Weak transcription	Gastric	stomach
24	chr4:110601200-110615800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:110601400-110608400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:110601400-110610800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr4:110601600-110608600	Weak transcription	Placenta	Placenta
28	chr4:110601600-110611000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:110601600-110613400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:110601800-110622800	Weak transcription	Right Atrium	heart
31	chr4:110602200-110611800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:110602400-110612000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:110602600-110612000	Weak transcription	NHLF	lung
34	chr4:110602600-110620000	Weak transcription	Small Intestine	intestine
35	chr4:110602800-110609000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:110603000-110610200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:110603000-110611400	Weak transcription	Pancreas	Pancrea
38	chr4:110603200-110611800	Weak transcription	Brain Anterior Caudate	brain
39	chr4:110603400-110612000	Weak transcription	Aorta	Aorta
40	chr4:110603800-110609400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:110603800-110611000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:110604200-110608400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:110604200-110608600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:110604200-110608600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:110604200-110611400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:110604200-110611400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr4:110604200-110611400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr4:110604200-110611400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:110604200-110612000	Weak transcription	HMEC	breast
50	chr4:110604200-110613400	Weak transcription	Osteobl	bone

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