Variant report

Variant	rs6857252
Chromosome Location	chr4:110611355-110611356
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110350104..110351990-chr4:110609862..110612756,2	K562	blood:
2	chr4:110608213..110611380-chr4:110623031..110625861,3	K562	blood:
3	chr4:110350104..110352430-chr4:110610795..110612756,2	K562	blood:
4	chr4:110609534..110611463-chr4:110619713..110622437,2	K562	blood:

Variant related genes	Relation type
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12513113	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13846	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1543812	0.83[AMR][1000 genomes]
rs2158204	0.83[AMR][1000 genomes]
rs62327660	0.81[EUR][1000 genomes]
rs6533446	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6824270	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6824542	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6858416	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7658262	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7690921	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6857252	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
2	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
3	chr4:110592000-110611600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:110593800-110611600	Weak transcription	K562	blood
5	chr4:110598800-110622800	Weak transcription	NHEK	skin
6	chr4:110599400-110611400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:110600000-110611400	Weak transcription	Spleen	Spleen
8	chr4:110600200-110613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:110600400-110611800	Weak transcription	NHDF-Ad	bronchial
10	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:110601200-110611400	Weak transcription	Gastric	stomach
12	chr4:110601200-110615800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:110601600-110613400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:110601800-110622800	Weak transcription	Right Atrium	heart
15	chr4:110602200-110611800	Weak transcription	Brain Germinal Matrix	brain
16	chr4:110602400-110612000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:110602600-110612000	Weak transcription	NHLF	lung
18	chr4:110602600-110620000	Weak transcription	Small Intestine	intestine
19	chr4:110603000-110611400	Weak transcription	Pancreas	Pancrea
20	chr4:110603200-110611800	Weak transcription	Brain Anterior Caudate	brain
21	chr4:110603400-110612000	Weak transcription	Aorta	Aorta
22	chr4:110604200-110611400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:110604200-110611400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:110604200-110611400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:110604200-110611400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:110604200-110612000	Weak transcription	HMEC	breast
27	chr4:110604200-110613400	Weak transcription	Osteobl	bone
28	chr4:110604200-110613800	Weak transcription	Right Ventricle	heart
29	chr4:110604400-110611400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:110604400-110611400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:110604400-110612000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:110604600-110611400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:110604600-110611600	Weak transcription	Fetal Kidney	kidney
34	chr4:110605000-110611800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:110605000-110613200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:110605000-110622800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:110605200-110619800	Strong transcription	Dnd41	blood
38	chr4:110605400-110612000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:110605400-110616000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr4:110605600-110611400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:110605600-110611400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:110605600-110611800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:110605600-110612400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:110605600-110612400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:110605600-110616000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr4:110605600-110619800	Strong transcription	Fetal Thymus	thymus
47	chr4:110605600-110622800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:110605800-110611400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:110605800-110611800	Weak transcription	Lung	lung
50	chr4:110605800-110619400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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