Variant report

Variant	rs13846
Chromosome Location	chr4:110605744-110605745
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1008327	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11734973	0.80[ASN][1000 genomes]
rs12513113	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128388	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1543812	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17440077	0.84[JPT][hapmap]
rs2158204	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346835	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4698770	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4698775	0.93[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62326057	0.81[ASN][1000 genomes]
rs62326058	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62327660	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533442	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6824270	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857252	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6858416	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72674829	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7658262	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7690921	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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
rs13846	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 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	chr4:110584200-110606000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:110584400-110608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:110585800-110608800	Weak transcription	Adipose Nuclei	Adipose
6	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
7	chr4:110590600-110606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:110591200-110608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:110592000-110611600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:110593000-110608200	Weak transcription	Fetal Lung	lung
11	chr4:110593800-110611600	Weak transcription	K562	blood
12	chr4:110597000-110605800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:110598400-110608200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:110598600-110610400	Weak transcription	HSMMtube	muscle
15	chr4:110598800-110611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:110598800-110622800	Weak transcription	NHEK	skin
17	chr4:110599400-110611400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:110600000-110610600	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:110600000-110611400	Weak transcription	Spleen	Spleen
20	chr4:110600200-110613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:110600400-110610000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:110600400-110610200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:110600400-110611800	Weak transcription	NHDF-Ad	bronchial
24	chr4:110600600-110611200	Weak transcription	HSMM	muscle
25	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:110601000-110606600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:110601000-110607400	Weak transcription	Fetal Stomach	stomach
28	chr4:110601000-110608400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:110601200-110610200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:110601200-110611400	Weak transcription	Gastric	stomach
31	chr4:110601200-110615800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr4:110601400-110608400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:110601400-110610800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr4:110601600-110608600	Weak transcription	Placenta	Placenta
35	chr4:110601600-110611000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:110601600-110613400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:110601800-110622800	Weak transcription	Right Atrium	heart
38	chr4:110602200-110611800	Weak transcription	Brain Germinal Matrix	brain
39	chr4:110602400-110612000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:110602600-110612000	Weak transcription	NHLF	lung
41	chr4:110602600-110620000	Weak transcription	Small Intestine	intestine
42	chr4:110602800-110609000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:110603000-110610200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:110603000-110611400	Weak transcription	Pancreas	Pancrea
45	chr4:110603200-110611800	Weak transcription	Brain Anterior Caudate	brain
46	chr4:110603400-110612000	Weak transcription	Aorta	Aorta
47	chr4:110603600-110607600	Weak transcription	Fetal Intestine Large	intestine
48	chr4:110603800-110609400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:110603800-110611000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:110604200-110608400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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