Variant report

Variant	rs11024482
Chromosome Location	chr11:18120647-18120648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18108743..18110773-chr11:18118441..18121392,2	K562	blood:
2	chr11:18119528..18121940-chr11:18122480..18124459,3	K562	blood:
3	chr11:18120429..18123330-chr11:18124710..18127285,2	K562	blood:
4	chr11:18032101..18034009-chr11:18120106..18122716,2	K562	blood:

Variant related genes	Relation type
ENSG00000166788	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10500831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832880	0.92[EUR][1000 genomes]
rs10832882	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024449	0.83[CEU][hapmap]
rs11024458	0.86[EUR][1000 genomes]
rs11024460	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024461	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11024468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024474	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11024476	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024478	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11024484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024489	0.88[ASN][1000 genomes]
rs11024493	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12360537	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12363226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12364327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12792460	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1399025	0.90[CHB][hapmap]
rs1975777	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2085275	0.82[CHB][hapmap]
rs2168361	0.94[ASN][1000 genomes]
rs2263407	0.86[ASN][1000 genomes]
rs2468832	0.80[ASN][1000 genomes]
rs2468841	0.86[ASN][1000 genomes]
rs2468842	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2956631	0.84[ASN][1000 genomes]
rs35447333	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741199	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs4052539	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs4756930	0.90[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap]
rs5790015	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61882530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486406	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs7117439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7118373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7119063	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7131255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131454	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7929920	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7933259	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7934091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7942794	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7943725	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7943884	0.96[EUR][1000 genomes]
rs871699	0.90[CHB][hapmap]
rs907922	0.90[CHB][hapmap]
rs907923	0.96[ASN][1000 genomes]
rs964834	0.90[CHB][hapmap];0.83[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11024482	SAAL1	cis	multi-tissue	Pritchard
rs11024482	SAAL1	cis	parietal	SCAN
rs11024482	SAAL1	cis	brain	seeQTL
rs11024482	SAAL1	cis	Artery Tibial	GTEx
rs11024482	SAAL1	cis	lymphoblastoid	seeQTL
rs11024482	SAAL1	cis	Adipose Subcutaneous	GTEx
rs11024482	TPH1	cis	cerebellum	SCAN
rs11024482	SAAL1	cis	lung	GTEx
rs11024482	SAAL1	cis	Thyroid	GTEx
rs11024482	MRGPRX3	cis	Esophagus Mucosa	GTEx
rs11024482	SAAL1	cis	Esophagus Muscularis	GTEx
rs11024482	SAAL1	cis	Skin Sun Exposed Lower leg	GTEx
rs11024482	SAAL1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18098200-18124400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:18099000-18125800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:18099800-18124800	Strong transcription	Dnd41	blood
4	chr11:18100200-18126200	Weak transcription	Small Intestine	intestine
5	chr11:18100400-18126000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:18100600-18125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:18100800-18126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:18101000-18122000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:18103400-18126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:18104800-18125200	Strong transcription	Primary T cells from cord blood	blood
11	chr11:18104800-18125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:18105400-18125800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:18107200-18126000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:18107400-18121600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:18107400-18125800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:18107600-18125400	Strong transcription	Fetal Muscle Leg	muscle
17	chr11:18107800-18126200	Weak transcription	NHDF-Ad	bronchial
18	chr11:18108200-18125200	Strong transcription	Primary B cells from cord blood	blood
19	chr11:18108600-18122800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:18110600-18126200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:18111000-18123600	Weak transcription	Aorta	Aorta
22	chr11:18111000-18126600	Weak transcription	Right Ventricle	heart
23	chr11:18111200-18125200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:18113000-18125600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:18113400-18125400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr11:18114200-18125400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:18115600-18123200	Weak transcription	Osteobl	bone
28	chr11:18115800-18126000	Weak transcription	Fetal Heart	heart
29	chr11:18116000-18122600	Weak transcription	Fetal Brain Male	brain
30	chr11:18116000-18122600	Weak transcription	A549	lung
31	chr11:18116000-18125800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:18116000-18126000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:18116000-18127000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:18116200-18121000	Weak transcription	Fetal Lung	lung
35	chr11:18116200-18121000	Weak transcription	NH-A	brain
36	chr11:18116200-18123400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:18116200-18123400	Weak transcription	Fetal Intestine Small	intestine
38	chr11:18116200-18126600	Weak transcription	Psoas Muscle	Psoas
39	chr11:18116400-18122600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:18116800-18122600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:18116800-18122600	Weak transcription	GM12878-XiMat	blood
42	chr11:18116800-18122800	Weak transcription	Spleen	Spleen
43	chr11:18116800-18123400	Weak transcription	NHLF	lung
44	chr11:18116800-18124800	Weak transcription	Pancreas	Pancrea
45	chr11:18117000-18126200	Weak transcription	Gastric	stomach
46	chr11:18117000-18126400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr11:18117600-18121200	Weak transcription	Left Ventricle	heart
48	chr11:18117600-18122400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:18117600-18122600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr11:18117600-18122600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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