Variant report

Variant	rs11689288
Chromosome Location	chr2:48730021-48730022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48727413..48730454-chr2:48730607..48734866,3	K562	blood:

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11675947	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11679685	0.80[AMR][1000 genomes]
rs11683444	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11687498	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11687771	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11689285	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11690526	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11693784	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2937	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34026270	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34242961	0.87[AFR][1000 genomes]
rs34542838	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4364065	0.80[AMR][1000 genomes]
rs7570877	0.86[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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11689288	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48689200-48735600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:48690000-48735600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
4	chr2:48695600-48735200	Weak transcription	K562	blood
5	chr2:48698800-48735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:48700200-48735400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:48700600-48735600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:48704000-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:48704600-48735400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:48704600-48735600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:48707400-48742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:48708400-48735400	Weak transcription	Stomach Mucosa	stomach
13	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:48710200-48745000	Weak transcription	Fetal Brain Male	brain
15	chr2:48710400-48735400	Weak transcription	NHLF	lung
16	chr2:48712400-48734200	Weak transcription	NHEK	skin
17	chr2:48714400-48735400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:48717800-48733200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:48720800-48735800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:48721000-48735600	Strong transcription	Fetal Thymus	thymus
21	chr2:48721000-48736400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:48721600-48731400	Strong transcription	Fetal Stomach	stomach
23	chr2:48722600-48741800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:48723800-48748200	Strong transcription	GM12878-XiMat	blood
25	chr2:48724200-48735000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:48724200-48735600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:48724400-48735400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:48724400-48738400	Weak transcription	Fetal Heart	heart
29	chr2:48725600-48733400	Strong transcription	Fetal Intestine Large	intestine
30	chr2:48726200-48735600	Weak transcription	Gastric	stomach
31	chr2:48726200-48735600	Weak transcription	Pancreas	Pancrea
32	chr2:48726200-48742400	Weak transcription	Colonic Mucosa	Colon
33	chr2:48726400-48731600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:48726400-48732400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:48726400-48734000	Weak transcription	Brain Angular Gyrus	brain
36	chr2:48726400-48734400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:48726400-48735600	Weak transcription	Small Intestine	intestine
38	chr2:48726400-48737800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:48726600-48735200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:48726600-48735600	Weak transcription	Fetal Kidney	kidney
42	chr2:48726800-48735200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:48727400-48735400	Weak transcription	NH-A	brain
44	chr2:48727400-48735600	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:48727600-48733000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:48728200-48734200	Weak transcription	Fetal Lung	lung
47	chr2:48728200-48756800	Weak transcription	HMEC	breast
48	chr2:48728400-48735200	Weak transcription	Hela-S3	cervix
49	chr2:48728600-48732800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:48728600-48732800	Weak transcription	Brain Hippocampus Middle	brain

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