Variant report

Variant	rs6486406
Chromosome Location	chr11:18105871-18105872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18105565..18107407-chr11:18114398..18116399,2	K562	blood:
2	chr11:18103887..18107035-chr11:18125471..18127692,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166788	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10500831	0.81[CEU][hapmap];0.80[CHD][hapmap];0.85[MEX][hapmap]
rs10741736	0.86[ASN][1000 genomes]
rs10832880	0.84[AFR][1000 genomes]
rs10832881	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11024460	0.81[CEU][hapmap]
rs11024467	0.86[ASN][1000 genomes]
rs11024469	0.86[ASN][1000 genomes]
rs11024470	0.90[ASN][1000 genomes]
rs11024472	0.86[ASN][1000 genomes]
rs11024474	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs11024475	0.86[ASN][1000 genomes]
rs11024477	0.90[ASN][1000 genomes]
rs11024478	0.86[ASN][1000 genomes]
rs11024480	0.86[ASN][1000 genomes]
rs11024482	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs11024485	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs11024487	0.86[ASN][1000 genomes]
rs11024488	0.86[ASN][1000 genomes]
rs11024491	0.88[ASN][1000 genomes]
rs11024492	0.88[ASN][1000 genomes]
rs12360537	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs12364327	0.81[CEU][hapmap];0.80[CHD][hapmap];0.85[MEX][hapmap]
rs12365158	0.86[ASN][1000 genomes]
rs12365751	0.86[ASN][1000 genomes]
rs1399025	0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs1980096	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1980097	0.86[ASN][1000 genomes]
rs2085275	0.92[JPT][hapmap]
rs2271533	0.86[ASN][1000 genomes]
rs2468842	0.80[CHD][hapmap]
rs3741199	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs4052539	0.80[CHD][hapmap]
rs4756930	0.81[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs4757613	0.86[ASN][1000 genomes]
rs56001925	0.86[ASN][1000 genomes]
rs61882529	0.86[ASN][1000 genomes]
rs7102017	0.86[ASN][1000 genomes]
rs7103885	0.90[ASN][1000 genomes]
rs7104168	0.90[ASN][1000 genomes]
rs7104856	0.90[ASN][1000 genomes]
rs7113855	0.88[ASN][1000 genomes]
rs7118250	0.86[ASN][1000 genomes]
rs7119063	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs7129345	0.88[ASN][1000 genomes]
rs7131255	0.81[CEU][hapmap];0.80[CHD][hapmap];0.85[MEX][hapmap]
rs7931522	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7934091	0.81[CEU][hapmap]
rs7936878	0.86[ASN][1000 genomes]
rs7942794	0.81[CEU][hapmap]
rs871699	0.81[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs907922	0.81[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs964833	0.86[ASN][1000 genomes]
rs964834	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs964835	0.86[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6486406	SAAL1	cis	parietal	SCAN
rs6486406	SAAL1	cis	cerebellum	SCAN
rs6486406	SAAL1	cis	Artery Tibial	GTEx
rs6486406	RPS13	cis	parietal	SCAN
rs6486406	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs6486406	TPH1	cis	cerebellum	SCAN

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	chr11:18086400-18107600	Weak transcription	Lung	lung
6	chr11:18087400-18109800	Weak transcription	Gastric	stomach
7	chr11:18087400-18115800	Weak transcription	Pancreas	Pancrea
8	chr11:18090200-18107600	Weak transcription	Aorta	Aorta
9	chr11:18092200-18107200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:18092800-18109400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:18093200-18106000	Weak transcription	Fetal Stomach	stomach
12	chr11:18094200-18108400	Weak transcription	Brain Substantia Nigra	brain
13	chr11:18094600-18107600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:18094800-18107600	Weak transcription	Esophagus	oesophagus
15	chr11:18096400-18106000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:18096400-18118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:18097600-18107600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:18098200-18124400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:18098400-18107600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:18099000-18125800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:18099200-18107800	Weak transcription	Brain Angular Gyrus	brain
22	chr11:18099200-18114200	Weak transcription	Fetal Heart	heart
23	chr11:18099600-18114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:18099800-18106600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:18099800-18106600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:18099800-18118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:18099800-18124800	Strong transcription	Dnd41	blood
28	chr11:18100200-18108400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr11:18100200-18126200	Weak transcription	Small Intestine	intestine
30	chr11:18100400-18110400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr11:18100400-18118600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:18100400-18126000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:18100600-18106200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:18100600-18106800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:18100600-18109000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:18100600-18109800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:18100600-18117600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:18100600-18118200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:18100600-18125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:18100800-18106200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:18100800-18126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:18101000-18106200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr11:18101000-18112200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:18101000-18122000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr11:18101400-18108200	Weak transcription	Brain Anterior Caudate	brain
46	chr11:18101600-18114400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr11:18102000-18106600	Strong transcription	Fetal Intestine Large	intestine
48	chr11:18102200-18117800	Strong transcription	HSMM	muscle
49	chr11:18102400-18106000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:18102400-18118400	Strong transcription	Primary T cells fromperipheralblood	blood

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