Variant report

Variant	rs12363226
Chromosome Location	chr11:18108492-18108493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10500831	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832880	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10832882	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024458	0.86[EUR][1000 genomes]
rs11024460	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024461	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024468	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024476	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024482	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024484	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024485	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024489	0.90[ASN][1000 genomes]
rs11024493	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12364327	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792460	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1824017	0.80[ASN][1000 genomes]
rs1975777	0.83[ASN][1000 genomes]
rs2168361	0.96[ASN][1000 genomes]
rs2263407	0.88[ASN][1000 genomes]
rs2468832	0.82[ASN][1000 genomes]
rs2468841	0.88[ASN][1000 genomes]
rs2468842	0.88[ASN][1000 genomes]
rs2956631	0.86[ASN][1000 genomes]
rs35447333	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4052539	0.96[ASN][1000 genomes]
rs5790015	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882530	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117439	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7118373	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7131255	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131454	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929920	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7933259	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7934091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942794	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7943725	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7943884	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs907923	0.98[ASN][1000 genomes]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12363226	SAAL1	cis	Thyroid	GTEx
rs12363226	SAAL1	cis	Artery Tibial	GTEx
rs12363226	SAAL1	cis	lung	GTEx
rs12363226	MRGPRX3	cis	Esophagus Mucosa	GTEx
rs12363226	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12363226	SAAL1	cis	Esophagus Muscularis	GTEx
rs12363226	SAAL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12363226	SAAL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18083200-18109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr11:18085200-18113000	Weak transcription	Fetal Brain Male	brain
3	chr11:18085800-18109600	Weak transcription	Spleen	Spleen
4	chr11:18087400-18109800	Weak transcription	Gastric	stomach
5	chr11:18087400-18115800	Weak transcription	Pancreas	Pancrea
6	chr11:18092800-18109400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:18096400-18118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:18098200-18124400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:18099000-18125800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:18099200-18114200	Weak transcription	Fetal Heart	heart
11	chr11:18099600-18114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:18099800-18118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:18099800-18124800	Strong transcription	Dnd41	blood
14	chr11:18100200-18126200	Weak transcription	Small Intestine	intestine
15	chr11:18100400-18110400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:18100400-18118600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:18100400-18126000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:18100600-18109000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:18100600-18109800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:18100600-18117600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:18100600-18118200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:18100600-18125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:18100800-18126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:18101000-18112200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:18101000-18122000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:18101600-18114400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:18102200-18117800	Strong transcription	HSMM	muscle
28	chr11:18102400-18118400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:18103000-18109200	Weak transcription	Fetal Kidney	kidney
30	chr11:18103000-18114000	Weak transcription	HSMMtube	muscle
31	chr11:18103200-18108600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:18103200-18114600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:18103400-18109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:18103400-18110400	Weak transcription	Fetal Brain Female	brain
35	chr11:18103400-18112600	Weak transcription	Psoas Muscle	Psoas
36	chr11:18103400-18126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:18103600-18109600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:18103600-18110200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr11:18103800-18109600	Weak transcription	K562	blood
40	chr11:18104600-18111600	Strong transcription	Liver	Liver
41	chr11:18104800-18111600	Strong transcription	Placenta	Placenta
42	chr11:18104800-18125200	Strong transcription	Primary T cells from cord blood	blood
43	chr11:18104800-18125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:18105000-18110200	Strong transcription	Ovary	ovary
45	chr11:18105000-18112200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:18105000-18118200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:18105000-18118400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr11:18105200-18118200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr11:18105200-18118400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr11:18105200-18118600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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