Variant report

Variant	rs1404176
Chromosome Location	chr2:100358651-100358652
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10167011	0.84[AFR][1000 genomes]
rs10175788	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10182690	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10191077	0.82[ASN][1000 genomes]
rs10191816	0.98[ASN][1000 genomes]
rs10198310	0.83[EUR][1000 genomes]
rs10199548	0.80[AMR][1000 genomes]
rs10199818	1.00[ASN][1000 genomes]
rs11123793	0.96[ASN][1000 genomes]
rs11123794	0.98[ASN][1000 genomes]
rs11123795	0.98[ASN][1000 genomes]
rs11682978	0.98[ASN][1000 genomes]
rs11690403	0.98[ASN][1000 genomes]
rs11888741	1.00[ASN][1000 genomes]
rs12712059	0.98[ASN][1000 genomes]
rs13010551	1.00[ASN][1000 genomes]
rs13030932	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13407928	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13428668	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366761	0.83[EUR][1000 genomes]
rs1404175	0.98[ASN][1000 genomes]
rs1404177	0.98[ASN][1000 genomes]
rs1464757	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2030690	0.84[ASN][1000 genomes]
rs2049400	0.82[CEU][hapmap]
rs2091150	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2115601	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2163044	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309690	1.00[ASN][1000 genomes]
rs2309729	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2871316	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34116173	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34369751	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3863005	0.98[ASN][1000 genomes]
rs3863006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3915083	0.98[ASN][1000 genomes]
rs4332968	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4850914	0.95[ASN][1000 genomes]
rs4851225	1.00[ASN][1000 genomes]
rs4851226	1.00[ASN][1000 genomes]
rs4851228	0.98[ASN][1000 genomes]
rs4851229	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851230	0.98[ASN][1000 genomes]
rs4851232	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4851234	0.89[ASN][1000 genomes]
rs62150081	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6542890	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542891	0.86[ASN][1000 genomes]
rs6542903	0.82[AMR][1000 genomes]
rs6705966	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6708339	0.82[ASN][1000 genomes]
rs6721652	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732358	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6739478	0.98[ASN][1000 genomes]
rs6739601	1.00[ASN][1000 genomes]
rs6741990	0.98[ASN][1000 genomes]
rs6742650	0.81[AMR][1000 genomes]
rs6744510	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6746146	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6748557	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6756009	0.98[ASN][1000 genomes]
rs6756821	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757262	0.98[ASN][1000 genomes]
rs6758027	0.98[ASN][1000 genomes]
rs7559975	0.98[ASN][1000 genomes]
rs7561009	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7565155	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7566083	0.83[EUR][1000 genomes]
rs7573572	0.87[ASN][1000 genomes]
rs7582469	0.98[ASN][1000 genomes]
rs7584365	0.96[ASN][1000 genomes]
rs7589376	0.86[ASN][1000 genomes]
rs7602699	0.88[ASN][1000 genomes]
rs7604536	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs868665	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9308829	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs940458	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1404176	C2orf15	cis	cerebellum	SCAN
rs1404176	IL1RL1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100344000-100360200	Weak transcription	Brain Germinal Matrix	brain
2	chr2:100346200-100379400	Weak transcription	Fetal Lung	lung
3	chr2:100346400-100359400	Weak transcription	Ovary	ovary
4	chr2:100346800-100359600	Weak transcription	Fetal Brain Male	brain
5	chr2:100347400-100361600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:100348200-100359000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:100355800-100358800	Weak transcription	Primary B cells from cord blood	blood
8	chr2:100356600-100361000	Weak transcription	Fetal Stomach	stomach
9	chr2:100356600-100370400	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:100357000-100359200	Weak transcription	Fetal Thymus	thymus
11	chr2:100357600-100359200	Weak transcription	Liver	Liver
12	chr2:100357600-100369200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:100357600-100389400	Weak transcription	Thymus	Thymus
14	chr2:100357800-100361800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:100358200-100359800	Weak transcription	Fetal Brain Female	brain
16	chr2:100358200-100370000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:100358400-100359400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr2:100358400-100359800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:100358400-100370000	Weak transcription	Spleen	Spleen
20	chr2:100358400-100375400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:100358600-100358800	ZNF genes & repeats	Left Ventricle	heart
22	chr2:100358600-100360000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:100358600-100360000	Strong transcription	Dnd41	blood
24	chr2:100358600-100360200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:100358600-100360400	Strong transcription	Primary T cells from cord blood	blood
26	chr2:100358600-100370000	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links