Variant report

Variant	rs11039266
Chromosome Location	chr11:47532395-47532396
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	chr11:47531749..47534788-chr11:47570653..47573178,3	K562	blood:
2	chr11:47531412..47534315-chr11:47879046..47881492,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10769288	0.87[JPT][hapmap]
rs10838703	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap]
rs10838726	0.91[CEU][hapmap]
rs11039284	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039290	0.91[CEU][hapmap]
rs11039332	0.82[CEU][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap]
rs11606287	0.85[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap]
rs12224672	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12225051	0.90[AMR][1000 genomes]
rs12361415	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12577643	0.88[CEU][hapmap]
rs2278890	0.92[CHB][hapmap]
rs2280231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes]
rs2293576	1.00[ASW][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap]
rs3824869	0.85[CHB][hapmap]
rs61895112	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485758	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs7103835	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7118178	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes]
rs7120548	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs7933019	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11039266	MTCH2	cis	cerebellum	SCAN
rs11039266	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11039266	ACCSL	cis	parietal	SCAN
rs11039266	MADD	cis	parietal	SCAN
rs11039266	C1QTNF4	cis	multi-tissue	Pritchard
rs11039266	C1QTNF4	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47509000-47534400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:47510200-47536800	Weak transcription	Fetal Kidney	kidney
3	chr11:47521600-47534000	Weak transcription	Aorta	Aorta
4	chr11:47521600-47534400	Weak transcription	HUVEC	blood vessel
5	chr11:47522800-47536200	Weak transcription	Fetal Brain Female	brain
6	chr11:47523000-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:47523000-47545600	Weak transcription	Dnd41	blood
8	chr11:47524800-47549600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:47526400-47533400	Weak transcription	Fetal Stomach	stomach
10	chr11:47528000-47532400	Enhancers	Stomach Mucosa	stomach
11	chr11:47528000-47535000	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr11:47528000-47538200	Enhancers	Osteobl	bone
13	chr11:47528200-47532400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:47528400-47532600	Enhancers	Liver	Liver
15	chr11:47528400-47533400	Enhancers	Primary T cells from cord blood	blood
16	chr11:47528400-47536400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr11:47528400-47536800	Enhancers	Primary B cells from peripheral blood	blood
18	chr11:47528400-47544800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr11:47528800-47536600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:47528800-47541000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:47529000-47534400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr11:47529200-47534400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:47529200-47535000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:47529200-47536400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:47529200-47536600	Weak transcription	Brain Germinal Matrix	brain
26	chr11:47529400-47533800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:47529800-47534000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:47529800-47534200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr11:47529800-47534400	Weak transcription	Fetal Heart	heart
30	chr11:47529800-47534600	Enhancers	Psoas Muscle	Psoas
31	chr11:47530000-47534200	Weak transcription	Fetal Lung	lung
32	chr11:47530200-47543000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr11:47530400-47533200	Enhancers	HepG2	liver
34	chr11:47530400-47534200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:47530400-47534400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:47530800-47533400	Genic enhancers	NHEK	skin
37	chr11:47530800-47533600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr11:47530800-47533800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:47530800-47535200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:47530800-47538000	Enhancers	NHDF-Ad	bronchial
41	chr11:47531000-47533800	Enhancers	Lung	lung
42	chr11:47531000-47536000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:47531000-47536600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:47531200-47532400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:47531200-47532600	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:47531200-47532600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:47531200-47532600	Weak transcription	HSMMtube	muscle
48	chr11:47531200-47532800	Weak transcription	Primary B cells from cord blood	blood
49	chr11:47531200-47533000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:47531200-47533000	Enhancers	K562	blood

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