Variant report

Variant	rs7933259
Chromosome Location	chr11:18096260-18096261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18095890..18098789-chr11:18109246..18111081,2	K562	blood:
2	chr11:18096008..18098167-chr11:18099695..18101837,4	K562	blood:
3	chr11:18029098..18031772-chr11:18092202..18096288,3	K562	blood:
4	chr11:18094663..18097873-chr11:18099803..18103495,3	K562	blood:

Variant related genes	Relation type
ENSG00000166788	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10500831	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10832880	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832882	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024458	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024460	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11024461	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024468	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024476	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024482	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024484	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024485	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11024489	0.81[ASN][1000 genomes]
rs11024493	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12363226	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12364327	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12792460	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1975777	0.81[ASN][1000 genomes]
rs2168361	0.85[ASN][1000 genomes]
rs2263407	0.85[ASN][1000 genomes]
rs2468841	0.85[ASN][1000 genomes]
rs2468842	0.85[ASN][1000 genomes]
rs2956631	0.83[ASN][1000 genomes]
rs35447333	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4052539	0.85[ASN][1000 genomes]
rs5790015	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882530	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7117439	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7118373	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7131255	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7131454	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7929920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7934091	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7942794	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7943725	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943884	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907923	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv553591	chr11:18090519-18100022	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv553592	chr11:18095815-18099562	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv553593	chr11:18095815-18100022	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv553594	chr11:18095815-18100799	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7933259	SAAL1	cis	Skin Sun Exposed Lower leg	GTEx
rs7933259	SAAL1	cis	Esophagus Muscularis	GTEx
rs7933259	MRGPRX3	cis	Esophagus Mucosa	GTEx
rs7933259	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs7933259	SAAL1	cis	lung	GTEx
rs7933259	SAAL1	cis	Thyroid	GTEx
rs7933259	SAAL1	cis	Artery Tibial	GTEx
rs7933259	SAAL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18070800-18102600	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:18081400-18100400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr11:18083200-18109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr11:18083400-18102400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:18084800-18108400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:18085200-18097000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:18085200-18104200	Weak transcription	Fetal Intestine Small	intestine
8	chr11:18085200-18113000	Weak transcription	Fetal Brain Male	brain
9	chr11:18085600-18101000	Weak transcription	Thymus	Thymus
10	chr11:18085600-18102000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:18085800-18100600	Weak transcription	Fetal Kidney	kidney
12	chr11:18085800-18109600	Weak transcription	Spleen	Spleen
13	chr11:18086000-18100000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:18086000-18101000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:18086000-18105600	Weak transcription	Right Ventricle	heart
16	chr11:18086200-18100600	Weak transcription	Brain Anterior Caudate	brain
17	chr11:18086400-18107600	Weak transcription	Lung	lung
18	chr11:18086600-18100600	Weak transcription	Liver	Liver
19	chr11:18087400-18099800	Weak transcription	Dnd41	blood
20	chr11:18087400-18100600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:18087400-18109800	Weak transcription	Gastric	stomach
22	chr11:18087400-18115800	Weak transcription	Pancreas	Pancrea
23	chr11:18087600-18099800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:18087600-18100400	Weak transcription	HMEC	breast
25	chr11:18087600-18102400	Weak transcription	Brain Germinal Matrix	brain
26	chr11:18087600-18105200	Weak transcription	NHEK	skin
27	chr11:18087800-18100400	Weak transcription	Fetal Brain Female	brain
28	chr11:18087800-18100800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:18088200-18100800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:18088600-18100400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:18088800-18101200	Weak transcription	Ovary	ovary
32	chr11:18089200-18099800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:18089200-18102400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr11:18089600-18100800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:18089600-18101000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:18089600-18102600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:18089800-18099800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:18089800-18100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:18090000-18100600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:18090200-18107600	Weak transcription	Aorta	Aorta
41	chr11:18090400-18100600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:18090600-18100800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:18090800-18100600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:18090800-18101600	Weak transcription	GM12878-XiMat	blood
45	chr11:18091000-18100600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:18091400-18100600	Weak transcription	Primary T cells from cord blood	blood
47	chr11:18091600-18101000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr11:18091600-18101000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:18092200-18107200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:18092600-18102000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links