Variant report

Variant	rs1811388
Chromosome Location	chr2:110353910-110353911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10195867	1.00[ASN][1000 genomes]
rs1036317	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036318	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496432	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13006297	1.00[ASN][1000 genomes]
rs13412327	1.00[ASN][1000 genomes]
rs28441405	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28445980	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28464093	1.00[ASN][1000 genomes]
rs28553892	1.00[ASN][1000 genomes]
rs28570680	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28599496	0.96[ASN][1000 genomes]
rs28612440	0.84[EUR][1000 genomes]
rs28696274	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28719680	0.83[EUR][1000 genomes]
rs3213866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34111852	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34269507	1.00[ASN][1000 genomes]
rs34311530	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34441132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34517320	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34821058	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35120088	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35223862	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35392016	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35550721	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35955221	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4482487	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4953721	1.00[ASN][1000 genomes]
rs4953729	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4953730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4953788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4953847	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953848	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953849	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953853	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55794045	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56265736	0.82[EUR][1000 genomes]
rs56794190	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58031484	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6594050	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6594053	0.84[EUR][1000 genomes]
rs6594054	0.83[EUR][1000 genomes]
rs6709945	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6719215	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6725792	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6737736	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6751785	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6760577	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72824788	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72824789	0.96[ASN][1000 genomes]
rs72824796	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72824800	1.00[ASN][1000 genomes]
rs72824802	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72826816	0.82[EUR][1000 genomes]
rs72826817	0.83[EUR][1000 genomes]
rs753492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7565483	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7577865	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9330317	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9330321	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9750931	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9752531	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9798179	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1811388	SEPT10	cis	Liver	GTEx
rs1811388	ACOXL	cis	cerebellum	SCAN
rs1811388	10-Sep	cis	multi-tissue	Pritchard
rs1811388	RGL3	cis	Liver	GTEx
rs1811388	RGL3	trans	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
4	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
6	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
9	chr2:110324600-110362200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:110329000-110369000	Weak transcription	Ovary	ovary
11	chr2:110329200-110359400	Weak transcription	NHLF	lung
12	chr2:110329200-110369400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:110329400-110359600	Weak transcription	NHDF-Ad	bronchial
14	chr2:110338600-110354600	Weak transcription	Right Atrium	heart
15	chr2:110338600-110357600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:110341600-110359400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:110341800-110359000	Weak transcription	Fetal Kidney	kidney
18	chr2:110343400-110357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:110343400-110357600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:110343400-110358000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:110343400-110358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:110343400-110358600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:110343400-110358800	Weak transcription	Adipose Nuclei	Adipose
24	chr2:110343400-110362200	Weak transcription	Psoas Muscle	Psoas
25	chr2:110343400-110362200	Weak transcription	Osteobl	bone
26	chr2:110343600-110364400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:110344000-110357600	Weak transcription	Left Ventricle	heart
28	chr2:110344000-110358600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:110344400-110355000	Weak transcription	Aorta	Aorta
30	chr2:110344400-110358200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:110344400-110365800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:110344600-110362200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:110348600-110354000	Strong transcription	HepG2	liver
34	chr2:110348600-110357600	Weak transcription	Right Ventricle	heart
35	chr2:110348600-110359400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:110349200-110354600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:110349200-110355000	Weak transcription	Brain Angular Gyrus	brain
38	chr2:110349400-110362200	Weak transcription	Lung	lung
39	chr2:110349400-110364600	Weak transcription	HSMM	muscle
40	chr2:110349800-110354600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:110349800-110358600	Weak transcription	HUVEC	blood vessel
42	chr2:110349800-110359400	Weak transcription	Hela-S3	cervix
43	chr2:110349800-110362200	Weak transcription	A549	lung
44	chr2:110350200-110365800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:110350200-110367000	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:110350400-110362200	Weak transcription	Fetal Intestine Small	intestine
47	chr2:110350400-110363600	Weak transcription	Placenta	Placenta
48	chr2:110350400-110369200	Weak transcription	Fetal Stomach	stomach
49	chr2:110350800-110358600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:110352000-110362200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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