Variant report

Variant	rs3758672
Chromosome Location	chr11:47278417-47278418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47278014..47279566-chr11:47397375..47399995,2	K562	blood:
2	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
3	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
4	chr11:47198598..47200151-chr11:47277071..47279146,2	K562	blood:
5	chr11:47205592..47209017-chr11:47278399..47281373,5	MCF-7	breast:
6	chr11:47198332..47200151-chr11:47277071..47279374,2	K562	blood:
7	chr11:47277336..47279783-chr11:47290576..47292976,4	MCF-7	breast:
8	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
9	chr11:47277979..47283267-chr11:47289057..47293509,9	K562	blood:
10	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000066336	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10501321	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1052373	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1055510	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10742799	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10742801	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10769252	0.82[AMR][1000 genomes]
rs10838684	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838690	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10838691	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10838692	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10838693	0.85[EUR][1000 genomes]
rs11039156	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039166	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11039167	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12575456	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1375688	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1449627	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2013867	0.86[EUR][1000 genomes]
rs2167079	0.86[EUR][1000 genomes]
rs2279239	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs326214	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs326222	0.86[EUR][1000 genomes]
rs35879051	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3758669	0.87[EUR][1000 genomes]
rs3758673	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3781621	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3781622	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3816725	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3847502	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4752822	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4752824	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4752825	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4752980	0.86[EUR][1000 genomes]
rs59663860	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61896050	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6485746	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7109147	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7109203	0.82[EUR][1000 genomes]
rs7120118	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7120957	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7124955	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7127907	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7129661	0.87[EUR][1000 genomes]
rs7395581	0.84[EUR][1000 genomes]
rs7940809	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs830085	0.85[EUR][1000 genomes]
rs901746	0.86[EUR][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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3758672	PACSIN3	cis	Esophagus Mucosa	GTEx
rs3758672	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47271000-47280800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47271400-47278600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:47271400-47278600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:47271400-47278600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:47271400-47278600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:47271400-47278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:47271400-47278800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:47271400-47278800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:47271400-47278800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:47271400-47278800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:47271400-47278800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:47271400-47278800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:47271400-47278800	Weak transcription	Esophagus	oesophagus
14	chr11:47271400-47279000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:47271400-47279000	Weak transcription	Fetal Brain Female	brain
16	chr11:47271400-47279000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:47271400-47279200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:47271400-47281000	Weak transcription	Thymus	Thymus
19	chr11:47271400-47281200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr11:47271400-47281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:47271400-47281200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:47271400-47281200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:47271600-47279000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:47272000-47278600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:47272400-47286400	Weak transcription	Dnd41	blood
26	chr11:47275200-47279000	Enhancers	Fetal Muscle Leg	muscle
27	chr11:47275200-47279000	Enhancers	Right Atrium	heart
28	chr11:47275400-47279000	Enhancers	Placenta	Placenta
29	chr11:47275600-47278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:47275800-47279400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
32	chr11:47276200-47278600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:47276600-47278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:47276600-47279600	Weak transcription	Fetal Thymus	thymus
35	chr11:47276800-47278600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:47276800-47278600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:47276800-47278600	Weak transcription	A549	lung
38	chr11:47276800-47278800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:47276800-47278800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:47276800-47278800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:47276800-47278800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:47276800-47278800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr11:47276800-47278800	Weak transcription	Brain Germinal Matrix	brain
44	chr11:47276800-47278800	Weak transcription	Psoas Muscle	Psoas
45	chr11:47276800-47278800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:47276800-47278800	Weak transcription	Right Ventricle	heart
47	chr11:47276800-47280800	Weak transcription	HSMMtube	muscle
48	chr11:47277000-47278600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:47277000-47278600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:47277000-47278600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links