Variant report

Variant	rs5030594
Chromosome Location	chr4:110611198-110611199
allele	A/C
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: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

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

Chromatin state (count:121 , 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	chr4:110598800-110611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:110598800-110622800	Weak transcription	NHEK	skin
7	chr4:110599400-110611400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:110600000-110611400	Weak transcription	Spleen	Spleen
9	chr4:110600200-110613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:110600400-110611800	Weak transcription	NHDF-Ad	bronchial
11	chr4:110600600-110611200	Weak transcription	HSMM	muscle
12	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:110601200-110611400	Weak transcription	Gastric	stomach
14	chr4:110601200-110615800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:110601600-110613400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:110601800-110622800	Weak transcription	Right Atrium	heart
17	chr4:110602200-110611800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:110602400-110612000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:110602600-110612000	Weak transcription	NHLF	lung
20	chr4:110602600-110620000	Weak transcription	Small Intestine	intestine
21	chr4:110603000-110611400	Weak transcription	Pancreas	Pancrea
22	chr4:110603200-110611800	Weak transcription	Brain Anterior Caudate	brain
23	chr4:110603400-110612000	Weak transcription	Aorta	Aorta
24	chr4:110604200-110611400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:110604200-110611400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:110604200-110611400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:110604200-110611400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:110604200-110612000	Weak transcription	HMEC	breast
29	chr4:110604200-110613400	Weak transcription	Osteobl	bone
30	chr4:110604200-110613800	Weak transcription	Right Ventricle	heart
31	chr4:110604400-110611400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:110604400-110611400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:110604400-110612000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:110604600-110611400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:110604600-110611600	Weak transcription	Fetal Kidney	kidney
36	chr4:110605000-110611200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:110605000-110611800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:110605000-110613200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:110605000-110622800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:110605200-110619800	Strong transcription	Dnd41	blood
41	chr4:110605400-110612000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:110605400-110616000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr4:110605600-110611400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:110605600-110611400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:110605600-110611800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:110605600-110612400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:110605600-110612400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:110605600-110616000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr4:110605600-110619800	Strong transcription	Fetal Thymus	thymus
50	chr4:110605600-110622800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links