Variant report

Variant	rs10501320
Chromosome Location	chr11:47293799-47293800
allele	C/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	MEF2A	chr11:47293513-47294118	K562	blood:	n/a	chr11:47293759-47293780 chr11:47293765-47293776 chr11:47293766-47293775 chr11:47293759-47293780 chr11:47293763-47293778 chr11:47293763-47293778
2	MEF2A	chr11:47293424-47294098	K562	blood:	n/a	chr11:47293759-47293780 chr11:47293765-47293776 chr11:47293766-47293775 chr11:47293759-47293780 chr11:47293763-47293778 chr11:47293763-47293778
3	SIN3AK20	chr11:47293474-47293871	K562	blood:	n/a	n/a
4	RUNX3	chr11:47293499-47293940	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:47293371-47294177	K562	blood:	n/a	n/a
6	ZMIZ1	chr11:47293761-47294070	K562	blood:	n/a	n/a
7	CBX3	chr11:47293481-47294111	K562	blood:	n/a	n/a
8	BHLHE40	chr11:47293716-47294073	K562	blood:	n/a	chr11:47293993-47294009
9	CTCF	chr11:47293680-47293830	WERI-Rb-1	eye:	n/a	chr11:47293820-47293828 chr11:47293821-47293829
10	MEF2A	chr11:47293493-47293945	GM12878	blood:	n/a	chr11:47293759-47293780 chr11:47293765-47293776 chr11:47293766-47293775 chr11:47293759-47293780 chr11:47293763-47293778 chr11:47293763-47293778
11	REST	chr11:47293798-47294917	ECC-1	luminal epithelium:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463
12	RUNX3	chr11:47293500-47294010	GM12878	blood:	n/a	n/a
13	MAZ	chr11:47293559-47293893	K562	blood:	n/a	n/a
14	MAZ	chr11:47293455-47293864	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:47293582-47294110	K562	blood:	n/a	n/a
16	MAX	chr11:47293494-47293826	K562	blood:	n/a	n/a
17	RCOR1	chr11:47293593-47294069	K562	blood:	n/a	n/a
18	TEAD4	chr11:47293411-47294226	K562	blood:	n/a	n/a
19	REST	chr11:47293529-47294141	K562	blood:	n/a	n/a
20	CHD2	chr11:47293792-47293818	GM12878	blood:	n/a	n/a
21	MEF2C	chr11:47293399-47293911	GM12878	blood:	n/a	chr11:47293759-47293780 chr11:47293765-47293776 chr11:47293766-47293775 chr11:47293759-47293780 chr11:47293763-47293778
22	TBL1XR1	chr11:47293576-47293937	K562	blood:	n/a	n/a
23	TAL1	chr11:47293537-47294190	K562	blood:	n/a	n/a
24	TBP	chr11:47293607-47293872	K562	blood:	n/a	n/a
25	REST	chr11:47293506-47294886	HL-60	blood:	n/a	chr11:47294443-47294463 chr11:47294444-47294462 chr11:47294443-47294457 chr11:47294443-47294463 chr11:47294443-47294463

No.	Distal block	Cell Line	Cell type
1	chr11:47267881..47272421-chr11:47288787..47294481,12	K562	blood:
2	chr11:47194502..47201735-chr11:47289181..47294156,14	K562	blood:
3	chr11:47291353..47293892-chr11:47343454..47345274,2	K562	blood:
4	chr11:47289567..47294786-chr11:47310778..47315538,7	MCF-7	breast:
5	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
6	chr11:47293111..47295014-chr11:47788351..47790710,2	MCF-7	breast:
7	chr11:47291588..47294118-chr11:47313687..47316370,3	K562	blood:
8	chr11:47268303..47273264-chr11:47289525..47294481,12	K562	blood:
9	chr11:47205837..47210171-chr11:47289770..47293955,7	MCF-7	breast:
10	chr11:47290389..47294105-chr11:47428413..47432863,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256746	TF binding region
MADD	TF binding region
ENSG00000025434	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000109920	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11039149	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs11039154	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11039165	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11039182	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7944419	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7944584	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[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	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
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Proinsulin levels	21873549	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10501320	ARFGAP2	cis	brain	BrainEAC
rs10501320	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47290600-47294000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr11:47292200-47293800	Flanking Active TSS	Brain Anterior Caudate	brain
3	chr11:47292200-47293800	Flanking Active TSS	Dnd41	blood
4	chr11:47292200-47294000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr11:47292200-47294000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr11:47292200-47294200	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr11:47292200-47294200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr11:47292200-47294200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:47292200-47294200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:47292200-47294200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr11:47292200-47294200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr11:47292200-47294400	Flanking Active TSS	K562	blood
13	chr11:47292400-47293800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr11:47292400-47294000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr11:47292400-47294000	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr11:47292400-47294000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr11:47292400-47294200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr11:47292600-47294000	Enhancers	Spleen	Spleen
19	chr11:47292600-47294200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:47292600-47294200	Enhancers	Gastric	stomach
21	chr11:47292600-47294200	Enhancers	Small Intestine	intestine
22	chr11:47292600-47294600	Enhancers	Liver	Liver
23	chr11:47292600-47294800	Enhancers	Psoas Muscle	Psoas
24	chr11:47292600-47294800	Enhancers	Stomach Mucosa	stomach
25	chr11:47292600-47295800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr11:47292600-47296000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:47292600-47296000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:47292600-47296000	Weak transcription	Ovary	ovary
29	chr11:47292600-47296200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:47292800-47293800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:47292800-47293800	Enhancers	Pancreas	Pancrea
32	chr11:47292800-47294000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr11:47292800-47294200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr11:47292800-47294200	Enhancers	Fetal Lung	lung
35	chr11:47292800-47294200	Enhancers	Fetal Stomach	stomach
36	chr11:47292800-47294600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:47292800-47294600	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr11:47292800-47294800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:47292800-47294800	Flanking Active TSS	GM12878-XiMat	blood
40	chr11:47292800-47295200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr11:47292800-47296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:47292800-47296200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:47293000-47293800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr11:47293000-47293800	Enhancers	NHEK	skin
45	chr11:47293000-47294000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr11:47293000-47294000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:47293000-47294000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:47293000-47294200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr11:47293000-47294200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr11:47293000-47294200	Enhancers	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links