Variant report

Variant	rs7942794
Chromosome Location	chr11:18106069-18106070
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: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10500831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10832880	0.92[EUR][1000 genomes]
rs10832882	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11024449	0.83[CEU][hapmap]
rs11024458	0.86[EUR][1000 genomes]
rs11024460	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024461	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11024468	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024476	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024482	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024484	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024493	0.89[EUR][1000 genomes]
rs12363226	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12364327	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12792460	0.85[EUR][1000 genomes]
rs1399025	0.81[MEX][hapmap]
rs1975777	0.83[CEU][hapmap]
rs2468842	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs35447333	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4052539	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs5790015	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61882530	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6486406	0.81[CEU][hapmap]
rs7117439	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118373	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131255	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7131454	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7929920	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7933259	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7934091	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7943725	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7943884	0.96[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7942794	SAAL1	cis	Adipose Subcutaneous	GTEx
rs7942794	SAAL1	cis	Artery Tibial	GTEx
rs7942794	SAAL1	cis	Skin Sun Exposed Lower leg	GTEx
rs7942794	SAAL1	cis	parietal	SCAN
rs7942794	SAAL1	cis	cerebellum	SCAN
rs7942794	SAAL1	cis	lung	GTEx
rs7942794	TPH1	cis	cerebellum	SCAN
rs7942794	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs7942794	SAAL1	cis	lymphoblastoid	seeQTL
rs7942794	MRGPRX3	cis	Esophagus Mucosa	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	chr11:18084800-18108400	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	chr11:18094200-18108400	Weak transcription	Brain Substantia Nigra	brain
12	chr11:18094600-18107600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:18094800-18107600	Weak transcription	Esophagus	oesophagus
14	chr11:18096400-18118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:18097600-18107600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:18098200-18124400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:18098400-18107600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:18099000-18125800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:18099200-18107800	Weak transcription	Brain Angular Gyrus	brain
20	chr11:18099200-18114200	Weak transcription	Fetal Heart	heart
21	chr11:18099600-18114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:18099800-18106600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:18099800-18106600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:18099800-18118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:18099800-18124800	Strong transcription	Dnd41	blood
26	chr11:18100200-18108400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:18100200-18126200	Weak transcription	Small Intestine	intestine
28	chr11:18100400-18110400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr11:18100400-18118600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:18100400-18126000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:18100600-18106200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:18100600-18106800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:18100600-18109000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:18100600-18109800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr11:18100600-18117600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:18100600-18118200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:18100600-18125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:18100800-18106200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:18100800-18126000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:18101000-18106200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr11:18101000-18112200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:18101000-18122000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:18101400-18108200	Weak transcription	Brain Anterior Caudate	brain
44	chr11:18101600-18114400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:18102000-18106600	Strong transcription	Fetal Intestine Large	intestine
46	chr11:18102200-18117800	Strong transcription	HSMM	muscle
47	chr11:18102400-18118400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr11:18102800-18107800	Weak transcription	Colon Smooth Muscle	Colon
49	chr11:18102800-18108400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:18102800-18108400	Weak transcription	Placenta Amnion	Placenta Amnion

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