Variant report

Variant	rs1560406
Chromosome Location	chr11:121238585-121238586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10750189	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10750190	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750191	0.81[AMR][1000 genomes]
rs10790438	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10790439	0.87[ASN][1000 genomes]
rs10790440	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10790443	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10892740	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10892741	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10892743	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10892744	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11218274	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11218281	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12575786	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1469535	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1560408	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1808581	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs190930	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs212501	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2453144	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2453145	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2512091	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297485	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs297486	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297489	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs297490	0.93[ASN][1000 genomes]
rs297491	0.93[ASN][1000 genomes]
rs297492	0.93[ASN][1000 genomes]
rs297493	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs297520	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs297525	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs297526	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935769	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4936619	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4936620	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61856965	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61903104	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs662738	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7102251	0.94[ASN][1000 genomes]
rs7117989	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7128176	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72991	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941466	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs891437	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs891438	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs903243	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs99672	0.93[ASN][1000 genomes]
rs99673	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1560406	SORL1	Cis_1M	lymphoblastoid	RTeQTL
rs1560406	C11orf32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121230800-121249800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:121236000-121239400	Enhancers	Brain Germinal Matrix	brain
3	chr11:121237000-121239400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr11:121237000-121239800	Enhancers	Fetal Thymus	thymus
5	chr11:121237200-121239200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:121237200-121239800	Enhancers	Fetal Kidney	kidney
7	chr11:121237200-121240000	Enhancers	Primary B cells from cord blood	blood
8	chr11:121237200-121240200	Enhancers	Ovary	ovary
9	chr11:121237400-121238600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr11:121237600-121238600	Enhancers	Colon Smooth Muscle	Colon
11	chr11:121237600-121238800	Flanking Active TSS	Dnd41	blood
12	chr11:121237600-121239000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr11:121237600-121239400	Enhancers	Rectal Smooth Muscle	rectum
14	chr11:121237600-121239600	Enhancers	Fetal Stomach	stomach
15	chr11:121237600-121240000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:121237600-121240200	Enhancers	Primary hematopoietic stem cells	blood
17	chr11:121237600-121240600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:121237800-121238600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:121237800-121238600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:121237800-121238600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr11:121237800-121238600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:121237800-121238600	Enhancers	Left Ventricle	heart
23	chr11:121237800-121238800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr11:121237800-121238800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:121237800-121239000	Enhancers	Small Intestine	intestine
26	chr11:121237800-121239200	Enhancers	Thymus	Thymus
27	chr11:121237800-121239400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:121237800-121239400	Enhancers	Fetal Intestine Small	intestine
29	chr11:121237800-121239800	Enhancers	Fetal Muscle Leg	muscle
30	chr11:121237800-121240000	Enhancers	Primary T cells from cord blood	blood
31	chr11:121237800-121240000	Flanking Active TSS	GM12878-XiMat	blood
32	chr11:121237800-121242600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:121238000-121238600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:121238000-121238600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr11:121238000-121238600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:121238000-121238600	Flanking Active TSS	Fetal Lung	lung
37	chr11:121238000-121238600	Enhancers	Right Atrium	heart
38	chr11:121238000-121238800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr11:121238000-121238800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:121238000-121238800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:121238000-121238800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr11:121238000-121239000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr11:121238000-121239200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr11:121238000-121242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:121238200-121238600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:121238200-121238600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr11:121238200-121238600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr11:121238200-121238600	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr11:121238200-121238600	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr11:121238200-121238600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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