Variant report

Variant	rs6485746
Chromosome Location	chr11:47286666-47286667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47286649-47287230	HUVEC	blood vessel:	n/a	n/a
2	YY1	chr11:47286654-47287037	K562	blood:	n/a	n/a
3	JUN	chr11:47285445-47287378	K562	blood:	n/a	chr11:47286935-47286944 chr11:47286212-47286219
4	GATA1	chr11:47285797-47287790	K562	blood:	n/a	chr11:47286372-47286389 chr11:47286928-47286938 chr11:47286353-47286362
5	TEAD4	chr11:47286186-47287173	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47270216..47272467-chr11:47284777..47286867,3	K562	blood:
2	chr11:47285533..47287740-chr11:47294426..47296494,3	K562	blood:
3	chr11:47284897..47288583-chr11:47288873..47294857,9	MCF-7	breast:
4	chr11:47280437..47283176-chr11:47284412..47287748,4	K562	blood:
5	chr11:47198981..47201647-chr11:47284713..47287592,2	K562	blood:
6	chr11:47270336..47272229-chr11:47286385..47288387,2	K562	blood:
7	chr11:47260942..47262867-chr11:47285650..47288524,2	MCF-7	breast:
8	chr11:47284460..47288493-chr11:47289509..47292662,6	K562	blood:
9	chr11:47197586..47200048-chr11:47285890..47288397,2	K562	blood:

Variant related genes	Relation type
MADD	TF binding region
NR1H3	TF binding region
ENSG00000256746	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000149182	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10501321	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1052373	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1055510	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10742799	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10742801	0.82[EUR][1000 genomes]
rs10769252	0.84[AMR][1000 genomes]
rs10838684	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838690	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10838691	0.82[EUR][1000 genomes]
rs10838692	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10838693	0.82[EUR][1000 genomes]
rs11039156	0.87[EUR][1000 genomes]
rs11039166	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11039167	0.80[EUR][1000 genomes]
rs12575456	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1375688	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1449627	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2013867	0.81[EUR][1000 genomes]
rs2279239	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs326214	0.84[EUR][1000 genomes]
rs326222	0.81[EUR][1000 genomes]
rs35879051	0.84[EUR][1000 genomes]
rs3758669	0.83[EUR][1000 genomes]
rs3758672	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3758673	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3781621	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3781622	0.81[EUR][1000 genomes]
rs3816725	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3847502	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4752822	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4752824	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4752825	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4752980	0.83[EUR][1000 genomes]
rs59663860	0.84[EUR][1000 genomes]
rs61896050	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7109203	0.80[EUR][1000 genomes]
rs7120118	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7120957	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7124955	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7127907	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7129661	0.82[EUR][1000 genomes]
rs7940809	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs901746	0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6485746	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs6485746	ACP2	cis	Thyroid	GTEx
rs6485746	PACSIN3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
2	chr11:47279200-47288800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:47279400-47286800	Weak transcription	NHEK	skin
4	chr11:47279400-47289400	Weak transcription	Fetal Brain Female	brain
5	chr11:47279800-47287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:47279800-47289800	Weak transcription	Esophagus	oesophagus
7	chr11:47280000-47289400	Weak transcription	Brain Angular Gyrus	brain
8	chr11:47280000-47289600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:47280000-47290000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:47280200-47289400	Weak transcription	Pancreas	Pancrea
11	chr11:47280200-47289600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:47280200-47289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:47280200-47289800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:47280200-47290600	Weak transcription	Ovary	ovary
15	chr11:47280200-47290800	Weak transcription	Aorta	Aorta
16	chr11:47280600-47289800	Weak transcription	Fetal Kidney	kidney
17	chr11:47281000-47289800	Weak transcription	Fetal Brain Male	brain
18	chr11:47281000-47290800	Weak transcription	Small Intestine	intestine
19	chr11:47281200-47286800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:47281200-47289000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:47281200-47289200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:47281200-47289400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:47281200-47289400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:47281200-47289400	Weak transcription	Fetal Lung	lung
25	chr11:47281200-47290000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:47281400-47288800	Weak transcription	Placenta	Placenta
27	chr11:47281400-47289400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:47281400-47289600	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:47281600-47286800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr11:47281600-47286800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr11:47281600-47286800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:47281600-47286800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:47281600-47287000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:47281600-47287000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr11:47281600-47287000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr11:47281600-47287200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:47281600-47289000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:47281600-47289400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:47281600-47289400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:47281600-47289400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:47281600-47289400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:47281600-47289600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:47281600-47289800	Weak transcription	Left Ventricle	heart
44	chr11:47281600-47289800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:47281600-47289800	Weak transcription	Right Atrium	heart
46	chr11:47281600-47289800	Weak transcription	A549	lung
47	chr11:47281800-47289400	Strong transcription	Fetal Intestine Large	intestine
48	chr11:47282000-47289600	Strong transcription	Fetal Stomach	stomach
49	chr11:47282000-47289800	Weak transcription	Colon Smooth Muscle	Colon
50	chr11:47282200-47289400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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