Variant report

Variant	rs1980097
Chromosome Location	chr11:18118146-18118147
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18117056..18118615-chr11:18121734..18123448,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10741736	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766453	0.98[EUR][1000 genomes]
rs10832881	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024462	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11024467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024470	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024474	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024477	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024478	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024480	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024488	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024489	0.86[ASN][1000 genomes]
rs11024491	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11024492	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12360537	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12365158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12365751	1.00[AFR][1000 genomes];1.00[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	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085275	0.84[EUR][1000 genomes]
rs2124378	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2271533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403246	0.94[EUR][1000 genomes]
rs3741199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287320	0.83[EUR][1000 genomes]
rs4756930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757613	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56001925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882526	0.81[AFR][1000 genomes]
rs61882529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486406	0.86[ASN][1000 genomes]
rs7102017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104168	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104856	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7106970	0.97[EUR][1000 genomes]
rs7113855	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7118250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129345	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7931522	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933593	0.93[EUR][1000 genomes]
rs7936469	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7936878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939791	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7943526	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7944348	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs871699	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs907922	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs964833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964835	0.99[AFR][1000 genomes];1.00[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
rs1980097	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs1980097	SAAL1	cis	Artery Tibial	GTEx
rs1980097	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	chr11:18098200-18124400	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	chr11:18099800-18118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:18099800-18124800	Strong transcription	Dnd41	blood
5	chr11:18100200-18126200	Weak transcription	Small Intestine	intestine
6	chr11:18100400-18118600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:18100400-18126000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:18100600-18118200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr11:18100600-18125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:18100800-18126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:18101000-18122000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:18102400-18118400	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr11:18103400-18126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:18104800-18125200	Strong transcription	Primary T cells from cord blood	blood
15	chr11:18104800-18125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:18105000-18118200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:18105000-18118400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:18105200-18118200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:18105200-18118400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:18105200-18118600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:18105400-18119000	Strong transcription	HMEC	breast
22	chr11:18105400-18125800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:18105800-18118600	Strong transcription	Fetal Thymus	thymus
24	chr11:18107200-18126000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:18107400-18118200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr11:18107400-18118400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:18107400-18121600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:18107400-18125800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:18107600-18118200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:18107600-18118400	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr11:18107600-18118600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:18107600-18125400	Strong transcription	Fetal Muscle Leg	muscle
33	chr11:18107800-18126200	Weak transcription	NHDF-Ad	bronchial
34	chr11:18108200-18125200	Strong transcription	Primary B cells from cord blood	blood
35	chr11:18108600-18122800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:18109400-18118200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:18110600-18119200	Strong transcription	Hela-S3	cervix
38	chr11:18110600-18126200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:18111000-18123600	Weak transcription	Aorta	Aorta
40	chr11:18111000-18126600	Weak transcription	Right Ventricle	heart
41	chr11:18111200-18125200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr11:18112400-18119000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr11:18112600-18118400	Strong transcription	NHEK	skin
44	chr11:18112800-18118400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:18113000-18118400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:18113000-18125600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr11:18113200-18118200	Strong transcription	Liver	Liver
48	chr11:18113200-18118200	Strong transcription	Ovary	ovary
49	chr11:18113200-18118400	Strong transcription	Placenta	Placenta
50	chr11:18113200-18119200	Strong transcription	Fetal Stomach	stomach

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