Variant report

Variant	rs11237240
Chromosome Location	chr11:77322805-77322806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77315212..77318257-chr11:77320880..77323907,4	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10899390	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11237226	0.81[ASN][1000 genomes]
rs11237230	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11237243	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237260	0.85[CHB][hapmap]
rs11237261	0.85[CHB][hapmap]
rs11237300	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11533286	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12221551	1.00[AFR][1000 genomes]
rs12225695	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12576652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17825097	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3019256	1.00[YRI][hapmap]
rs728130	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1038974	chr11:77284036-77431228	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1041384	chr11:77284558-77419809	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1048892	chr11:77290458-77431228	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv468641	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv555452	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv1035494	chr11:77309696-77431228	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11237240	HPS3	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77301400-77346000	Weak transcription	Small Intestine	intestine
2	chr11:77301600-77332800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:77301800-77326600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:77301800-77332200	Weak transcription	Esophagus	oesophagus
5	chr11:77301800-77345800	Weak transcription	Spleen	Spleen
6	chr11:77305600-77326000	Weak transcription	Primary B cells from cord blood	blood
7	chr11:77310800-77329200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:77311600-77327200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:77313000-77327200	Weak transcription	Psoas Muscle	Psoas
10	chr11:77313000-77345200	Weak transcription	Gastric	stomach
11	chr11:77313000-77347400	Weak transcription	Colonic Mucosa	Colon
12	chr11:77313200-77330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:77313400-77323400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr11:77313400-77327800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:77314000-77325800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:77314000-77330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:77314000-77345800	Weak transcription	Pancreas	Pancrea
18	chr11:77314000-77347400	Weak transcription	Fetal Heart	heart
19	chr11:77314200-77327200	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:77314200-77329200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:77314200-77329400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:77315000-77330800	Strong transcription	Liver	Liver
23	chr11:77315000-77341800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:77315200-77341400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:77315600-77341000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:77315800-77331600	Strong transcription	A549	lung
27	chr11:77316000-77326600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr11:77316400-77323800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:77316400-77338400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:77316400-77341400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:77316400-77346800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:77316600-77337200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:77316600-77344200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:77316600-77347000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:77317000-77326200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:77317000-77337400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:77317200-77330600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:77317200-77336800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:77317200-77337400	Strong transcription	Fetal Thymus	thymus
40	chr11:77317400-77323000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:77317400-77328400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:77317400-77331600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:77317400-77340200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr11:77317400-77340400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:77317600-77325200	Strong transcription	Hela-S3	cervix
46	chr11:77317600-77327200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:77317600-77330800	Strong transcription	Fetal Intestine Large	intestine
48	chr11:77317600-77337600	Strong transcription	Dnd41	blood
49	chr11:77318000-77337000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:77318600-77323000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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