Variant report

Variant	rs11024480
Chromosome Location	chr11:18115121-18115122
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18113148..18115855-chr11:18125984..18127640,2	MCF-7	breast:
2	chr11:18105565..18107407-chr11:18114398..18116399,2	K562	blood:
3	chr11:18114312..18117170-chr11:18118246..18120137,2	K562	blood:
4	chr11:18107232..18110048-chr11:18114396..18116772,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166788	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10741736	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766453	0.98[EUR][1000 genomes]
rs10832881	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024462	0.97[EUR][1000 genomes]
rs11024467	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024469	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024470	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024472	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024474	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024475	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024477	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024478	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024487	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024488	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024489	0.86[ASN][1000 genomes]
rs11024491	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11024492	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12360537	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12365158	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12365751	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417591	0.80[EUR][1000 genomes]
rs1399025	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1824018	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1980096	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980097	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085275	0.84[EUR][1000 genomes]
rs2124378	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2271533	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403246	0.94[EUR][1000 genomes]
rs3741199	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287320	0.83[EUR][1000 genomes]
rs4756930	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757613	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56001925	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882529	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486406	0.86[ASN][1000 genomes]
rs7102017	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103885	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104168	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104856	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7106970	0.97[EUR][1000 genomes]
rs7113855	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7118250	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119063	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129345	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7931522	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933593	0.93[EUR][1000 genomes]
rs7936469	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7936878	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939791	0.97[EUR][1000 genomes]
rs7943526	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7944348	0.97[EUR][1000 genomes]
rs871699	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907922	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs964833	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964834	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964835	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11024480	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs11024480	SAAL1	cis	Artery Tibial	GTEx
rs11024480	SERGEF	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18087400-18115800	Weak transcription	Pancreas	Pancrea
2	chr11:18096400-18118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:18098200-18124400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:18099000-18125800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:18099800-18118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:18099800-18124800	Strong transcription	Dnd41	blood
7	chr11:18100200-18126200	Weak transcription	Small Intestine	intestine
8	chr11:18100400-18118600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:18100400-18126000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:18100600-18117600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:18100600-18118200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:18100600-18125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr11:18100800-18126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:18101000-18122000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:18102200-18117800	Strong transcription	HSMM	muscle
16	chr11:18102400-18118400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr11:18103400-18126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:18104800-18125200	Strong transcription	Primary T cells from cord blood	blood
19	chr11:18104800-18125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:18105000-18118200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:18105000-18118400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:18105200-18118200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr11:18105200-18118400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:18105200-18118600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:18105400-18119000	Strong transcription	HMEC	breast
26	chr11:18105400-18125800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:18105800-18118600	Strong transcription	Fetal Thymus	thymus
28	chr11:18106000-18117800	Strong transcription	Adipose Nuclei	Adipose
29	chr11:18107200-18126000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:18107400-18115400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:18107400-18116200	Strong transcription	Fetal Lung	lung
32	chr11:18107400-18118200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr11:18107400-18118400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:18107400-18121600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:18107400-18125800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:18107600-18118200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:18107600-18118400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr11:18107600-18118600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:18107600-18125400	Strong transcription	Fetal Muscle Leg	muscle
40	chr11:18107800-18126200	Weak transcription	NHDF-Ad	bronchial
41	chr11:18108200-18115200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:18108200-18115200	Weak transcription	Fetal Intestine Small	intestine
43	chr11:18108200-18125200	Strong transcription	Primary B cells from cord blood	blood
44	chr11:18108400-18117600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:18108600-18117800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr11:18108600-18122800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:18109400-18117800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr11:18109400-18118200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:18109600-18115400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:18110200-18115200	Weak transcription	Fetal Kidney	kidney

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