Variant report

Variant	rs11024470
Chromosome Location	chr11:18104671-18104672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18034234..18035832-chr11:18102491..18104854,2	MCF-7	breast:
2	chr11:18103887..18107035-chr11:18125471..18127692,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166788	Chromatin interaction
ENSG00000129158	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10741736	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10766453	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10766457	0.80[EUR][1000 genomes]
rs1079785	0.81[AFR][1000 genomes]
rs10832881	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024462	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11024467	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024469	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024472	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024474	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024475	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024478	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024480	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024487	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024488	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024489	0.83[ASN][1000 genomes]
rs11024491	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024492	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12360537	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12365158	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12365751	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12417591	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1399025	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824018	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1980096	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980097	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085275	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2124378	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271533	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2403246	0.94[EUR][1000 genomes]
rs3741199	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4287320	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4756930	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4757613	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56001925	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61882529	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6486406	0.90[ASN][1000 genomes]
rs7102017	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7103885	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106970	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7110238	0.81[AFR][1000 genomes]
rs7113855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7118250	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7119063	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7129345	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7931522	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933593	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7936469	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7936878	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7937368	0.83[AFR][1000 genomes]
rs7939791	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7943526	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7944348	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs871699	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907922	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964833	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs964834	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs964835	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv553606	chr11:18098635-18105302	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11024470	SERGEF	Cis_1M	lymphoblastoid	RTeQTL
rs11024470	SAAL1	cis	Artery Tibial	GTEx
rs11024470	SAAL1	Cis_1M	lymphoblastoid	RTeQTL

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	chr11:18084800-18108400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:18085200-18113000	Weak transcription	Fetal Brain Male	brain
4	chr11:18085800-18109600	Weak transcription	Spleen	Spleen
5	chr11:18086000-18105600	Weak transcription	Right Ventricle	heart
6	chr11:18086400-18107600	Weak transcription	Lung	lung
7	chr11:18087400-18109800	Weak transcription	Gastric	stomach
8	chr11:18087400-18115800	Weak transcription	Pancreas	Pancrea
9	chr11:18087600-18105200	Weak transcription	NHEK	skin
10	chr11:18090200-18107600	Weak transcription	Aorta	Aorta
11	chr11:18092200-18107200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:18092800-18105800	Weak transcription	Left Ventricle	heart
13	chr11:18092800-18109400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:18093200-18106000	Weak transcription	Fetal Stomach	stomach
15	chr11:18094200-18108400	Weak transcription	Brain Substantia Nigra	brain
16	chr11:18094600-18107600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:18094800-18105600	Weak transcription	Hela-S3	cervix
18	chr11:18094800-18107600	Weak transcription	Esophagus	oesophagus
19	chr11:18096400-18106000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:18096400-18118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:18097200-18105600	Weak transcription	NHDF-Ad	bronchial
22	chr11:18097600-18107600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:18098200-18124400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr11:18098400-18107600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:18099000-18125800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:18099200-18107800	Weak transcription	Brain Angular Gyrus	brain
27	chr11:18099200-18114200	Weak transcription	Fetal Heart	heart
28	chr11:18099600-18114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:18099800-18106600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:18099800-18106600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:18099800-18118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:18099800-18124800	Strong transcription	Dnd41	blood
33	chr11:18100200-18108400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr11:18100200-18126200	Weak transcription	Small Intestine	intestine
35	chr11:18100400-18110400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr11:18100400-18118600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:18100400-18126000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr11:18100600-18106200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:18100600-18106800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:18100600-18109000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:18100600-18109800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr11:18100600-18117600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:18100600-18118200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:18100600-18125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:18100800-18106200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:18100800-18126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:18101000-18106200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr11:18101000-18112200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:18101000-18122000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:18101200-18105400	Weak transcription	HMEC	breast

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