Variant report

Variant	rs1124942
Chromosome Location	chr11:57316916-57316917
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12223229	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2234409	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2467328	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2467329	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2467330	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581930	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2649644	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649645	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649649	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2649651	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649653	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2649655	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649656	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2649659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649666	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2729358	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2729359	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2729367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2729369	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729370	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729373	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729375	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2729382	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848621	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848622	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2848624	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848638	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848639	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514385	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs722823	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1052073	chr11:57297499-57362802	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv541050	chr11:57297499-57362802	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1124942	SMTNL1	cis	Thyroid	GTEx
rs1124942	SMTNL1	cis	Esophagus Muscularis	GTEx
rs1124942	SMTNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs1124942	SMTNL1	cis	Artery Tibial	GTEx
rs1124942	SMTNL1	cis	Nerve Tibial	GTEx
rs1124942	SMTNL1	cis	lung	GTEx
rs1124942	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs1124942	SMTNL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57298800-57319200	Weak transcription	Small Intestine	intestine
2	chr11:57299000-57317000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:57299000-57317200	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:57299000-57317400	Weak transcription	Fetal Brain Male	brain
5	chr11:57299200-57317200	Weak transcription	Brain Angular Gyrus	brain
6	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
7	chr11:57299400-57317200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:57307200-57333600	Weak transcription	HMEC	breast
9	chr11:57309200-57333400	Weak transcription	Psoas Muscle	Psoas
10	chr11:57310800-57319200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:57311000-57317000	Weak transcription	Fetal Lung	lung
12	chr11:57311400-57317200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:57311400-57317200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:57311400-57317200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:57311400-57319800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:57311400-57320400	Weak transcription	Stomach Mucosa	stomach
17	chr11:57311600-57317000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:57311600-57317200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:57311600-57317200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:57311600-57319400	Weak transcription	Right Ventricle	heart
21	chr11:57311800-57317400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:57312200-57317000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:57312200-57319600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:57312400-57317200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:57312800-57317200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:57312800-57317400	Weak transcription	Colonic Mucosa	Colon
27	chr11:57313000-57326800	Strong transcription	Thymus	Thymus
28	chr11:57313200-57317200	Weak transcription	Brain Substantia Nigra	brain
29	chr11:57313200-57327600	Strong transcription	Fetal Brain Female	brain
30	chr11:57313200-57330000	Strong transcription	Dnd41	blood
31	chr11:57313400-57317000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:57313400-57327800	Strong transcription	Brain Germinal Matrix	brain
33	chr11:57313400-57328000	Strong transcription	Fetal Stomach	stomach
34	chr11:57313600-57323000	Strong transcription	Liver	Liver
35	chr11:57313600-57327800	Strong transcription	Fetal Thymus	thymus
36	chr11:57313600-57328600	Strong transcription	Lung	lung
37	chr11:57313800-57317400	Weak transcription	HSMMtube	muscle
38	chr11:57314000-57317200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:57314000-57326600	Strong transcription	Brain Anterior Caudate	brain
40	chr11:57314000-57328000	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr11:57314000-57328200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:57314000-57328600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:57314000-57330200	Strong transcription	Fetal Intestine Small	intestine
44	chr11:57314000-57330400	Strong transcription	Primary T cells from cord blood	blood
45	chr11:57314200-57317400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:57314200-57321400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:57314200-57323800	Strong transcription	Brain Hippocampus Middle	brain
48	chr11:57314200-57326400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:57314200-57329800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:57314400-57326600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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