Variant report

Variant	rs7129661
Chromosome Location	chr11:47268550-47268551
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47268548-47268781	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47197588..47201043-chr11:47267472..47270431,4	MCF-7	breast:
2	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
3	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:
4	chr11:47268303..47273264-chr11:47289525..47294481,12	K562	blood:
5	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
6	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
7	chr11:47201377..47203716-chr11:47267132..47269463,2	K562	blood:
8	chr11:47267881..47272421-chr11:47288787..47294481,12	K562	blood:
9	chr11:47197356..47201056-chr11:47268366..47272336,6	MCF-7	breast:

No data

Variant related genes	Relation type
ACP2	TF binding region
NR1H3	TF binding region
ENSG00000149182	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10501321	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1052373	0.82[EUR][1000 genomes]
rs1055510	0.86[EUR][1000 genomes]
rs10742799	0.86[EUR][1000 genomes]
rs10742801	0.84[EUR][1000 genomes]
rs10838681	0.90[AMR][1000 genomes]
rs10838684	0.88[EUR][1000 genomes]
rs10838690	0.85[EUR][1000 genomes]
rs10838691	0.84[EUR][1000 genomes]
rs10838692	0.84[EUR][1000 genomes]
rs10838693	0.84[EUR][1000 genomes]
rs11039156	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039166	0.85[EUR][1000 genomes]
rs11039167	0.82[EUR][1000 genomes]
rs12575456	0.85[EUR][1000 genomes]
rs1375688	0.85[EUR][1000 genomes]
rs1449627	0.86[EUR][1000 genomes]
rs2013867	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2167079	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279239	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs326214	0.86[EUR][1000 genomes]
rs326222	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35677603	0.84[ASN][1000 genomes]
rs35879051	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758669	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3758672	0.87[EUR][1000 genomes]
rs3758673	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3781621	0.85[EUR][1000 genomes]
rs3781622	0.84[EUR][1000 genomes]
rs3816725	0.86[EUR][1000 genomes]
rs3847502	0.85[EUR][1000 genomes]
rs4752822	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752824	0.85[EUR][1000 genomes]
rs4752825	0.84[EUR][1000 genomes]
rs4752980	0.85[EUR][1000 genomes]
rs59663860	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61896050	0.85[EUR][1000 genomes]
rs6485746	0.82[EUR][1000 genomes]
rs7109147	0.82[EUR][1000 genomes]
rs7109203	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7120118	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7120957	0.85[EUR][1000 genomes]
rs7124955	0.85[EUR][1000 genomes]
rs7127907	0.85[EUR][1000 genomes]
rs7395581	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7940809	0.85[EUR][1000 genomes]
rs830085	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs901746	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7129661	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs7129661	ACP2	cis	Thyroid	GTEx
rs7129661	PACSIN3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:47255400-47269200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:47255600-47268800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:47256800-47268800	Strong transcription	Fetal Thymus	thymus
7	chr11:47258000-47269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:47258600-47268800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:47259000-47268800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:47259000-47269000	Strong transcription	Fetal Stomach	stomach
11	chr11:47259400-47268800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr11:47259400-47268800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr11:47259400-47269000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr11:47259400-47269000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:47259600-47268600	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr11:47259600-47269000	Strong transcription	Fetal Muscle Leg	muscle
17	chr11:47260000-47268600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr11:47260000-47268600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:47260200-47269000	Strong transcription	Brain Substantia Nigra	brain
20	chr11:47260200-47269000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr11:47261000-47269000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:47261400-47268800	Weak transcription	Stomach Mucosa	stomach
23	chr11:47261600-47268800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr11:47261600-47269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:47261800-47268600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:47262000-47268600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:47264200-47268600	Weak transcription	Fetal Heart	heart
28	chr11:47264200-47268800	Strong transcription	Osteobl	bone
29	chr11:47264200-47269200	Weak transcription	Psoas Muscle	Psoas
30	chr11:47264400-47269000	Strong transcription	NHLF	lung
31	chr11:47264400-47269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:47264400-47269200	Weak transcription	HSMM	muscle
33	chr11:47264600-47269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:47264800-47269000	Weak transcription	Small Intestine	intestine
35	chr11:47265000-47268600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:47265200-47268600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:47265200-47268800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:47265400-47269000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:47265400-47269000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:47266000-47268600	Strong transcription	GM12878-XiMat	blood
41	chr11:47266000-47269000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:47266400-47268800	Genic enhancers	Adipose Nuclei	Adipose
43	chr11:47266400-47268800	Genic enhancers	Fetal Intestine Small	intestine
44	chr11:47266400-47269000	Genic enhancers	Fetal Intestine Large	intestine
45	chr11:47266600-47268800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:47266800-47268600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:47267000-47269200	Weak transcription	Fetal Brain Male	brain
48	chr11:47267000-47269400	Weak transcription	HSMMtube	muscle
49	chr11:47267200-47268800	Genic enhancers	HepG2	liver
50	chr11:47267200-47269200	Enhancers	Liver	Liver

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