Variant report

Variant	rs10500831
Chromosome Location	chr11:18102232-18102233
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	chr11:18102086..18103945-chr11:18110453..18114636,4	K562	blood:
2	chr11:18101916..18104550-chr11:18109024..18114636,6	K562	blood:

Variant related genes	Relation type
ENSG00000166788	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10832880	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10832882	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024449	0.83[CEU][hapmap]
rs11024458	0.86[EUR][1000 genomes]
rs11024460	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11024461	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11024468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024474	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11024476	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024478	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11024482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024485	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024489	0.90[ASN][1000 genomes]
rs11024493	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133758	1.00[LWK][hapmap]
rs12360537	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12363226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792460	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1399025	0.90[CHB][hapmap]
rs1824017	0.80[ASN][1000 genomes]
rs1975777	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2085275	0.82[CHB][hapmap]
rs2168361	0.96[ASN][1000 genomes]
rs2263407	0.88[ASN][1000 genomes]
rs2468832	0.82[ASN][1000 genomes]
rs2468841	0.88[ASN][1000 genomes]
rs2468842	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs2956631	0.86[ASN][1000 genomes]
rs35447333	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3741199	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs4052539	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs4756930	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]
rs5790015	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486406	0.81[CEU][hapmap];0.80[CHD][hapmap];0.85[MEX][hapmap]
rs7117439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7118373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7119063	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7131255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131454	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929920	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7933259	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7934091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942794	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]
rs7943725	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7943884	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs871699	0.90[CHB][hapmap]
rs907922	0.90[CHB][hapmap]
rs907923	0.98[ASN][1000 genomes]
rs964834	0.90[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv553605	chr11:18098635-18102232	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv553606	chr11:18098635-18105302	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv553612	chr11:18098688-18102232	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv553618	chr11:18098785-18102232	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv553626	chr11:18098932-18102232	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv553629	chr11:18098983-18102232	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10500831	SAAL1	cis	Thyroid	GTEx
rs10500831	SAAL1	cis	lymphoblastoid	seeQTL
rs10500831	SAAL1	cis	Adipose Subcutaneous	GTEx
rs10500831	MRGPRX3	cis	lesional skin	skin_eQTL
rs10500831	SAAL1	cis	parietal	SCAN
rs10500831	SAAL1	cis	lung	GTEx
rs10500831	MRGPRX3	cis	Esophagus Mucosa	GTEx
rs10500831	SAAL1	cis	Artery Tibial	GTEx
rs10500831	TPH1	cis	cerebellum	SCAN
rs10500831	SAAL1	cis	cerebellum	SCAN
rs10500831	SAAL1	cis	Esophagus Muscularis	GTEx
rs10500831	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs10500831	SAAL1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18070800-18102600	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:18083200-18109000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr11:18083400-18102400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:18084800-18108400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:18085200-18104200	Weak transcription	Fetal Intestine Small	intestine
6	chr11:18085200-18113000	Weak transcription	Fetal Brain Male	brain
7	chr11:18085800-18109600	Weak transcription	Spleen	Spleen
8	chr11:18086000-18105600	Weak transcription	Right Ventricle	heart
9	chr11:18086400-18107600	Weak transcription	Lung	lung
10	chr11:18087400-18109800	Weak transcription	Gastric	stomach
11	chr11:18087400-18115800	Weak transcription	Pancreas	Pancrea
12	chr11:18087600-18102400	Weak transcription	Brain Germinal Matrix	brain
13	chr11:18087600-18105200	Weak transcription	NHEK	skin
14	chr11:18089200-18102400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:18089600-18102600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:18090200-18107600	Weak transcription	Aorta	Aorta
17	chr11:18092200-18107200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:18092600-18102800	Weak transcription	NHLF	lung
19	chr11:18092800-18105800	Weak transcription	Left Ventricle	heart
20	chr11:18092800-18109400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:18093200-18106000	Weak transcription	Fetal Stomach	stomach
22	chr11:18094200-18108400	Weak transcription	Brain Substantia Nigra	brain
23	chr11:18094600-18107600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:18094800-18105600	Weak transcription	Hela-S3	cervix
25	chr11:18094800-18107600	Weak transcription	Esophagus	oesophagus
26	chr11:18096200-18102600	Weak transcription	HepG2	liver
27	chr11:18096400-18106000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:18096400-18118000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:18097200-18105600	Weak transcription	NHDF-Ad	bronchial
30	chr11:18097600-18107600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:18098200-18124400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr11:18098400-18107600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:18099000-18102600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:18099000-18125800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:18099200-18107800	Weak transcription	Brain Angular Gyrus	brain
36	chr11:18099200-18114200	Weak transcription	Fetal Heart	heart
37	chr11:18099400-18102400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:18099600-18102400	Weak transcription	HSMMtube	muscle
39	chr11:18099600-18114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:18099800-18103000	Strong transcription	Adipose Nuclei	Adipose
41	chr11:18099800-18103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:18099800-18103600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:18099800-18104000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:18099800-18106600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:18099800-18106600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:18099800-18118400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:18099800-18124800	Strong transcription	Dnd41	blood
48	chr11:18100000-18103400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:18100200-18102600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:18100200-18108400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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