Variant report

Variant	rs2309690
Chromosome Location	chr2:100373784-100373785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10175788	0.93[ASN][1000 genomes]
rs10182690	0.91[ASN][1000 genomes]
rs10191077	0.82[ASN][1000 genomes]
rs10191816	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10199818	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204617	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10496340	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10865032	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11123793	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123794	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123795	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123796	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11682978	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11690403	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11888741	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712059	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712060	0.83[AMR][1000 genomes]
rs13010551	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030932	0.93[ASN][1000 genomes]
rs13407928	0.93[ASN][1000 genomes]
rs13428668	0.98[ASN][1000 genomes]
rs1404175	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1404176	1.00[ASN][1000 genomes]
rs1404177	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464757	0.93[ASN][1000 genomes]
rs1568786	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2030690	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2091150	0.87[ASN][1000 genomes]
rs2115600	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2115601	0.91[ASN][1000 genomes]
rs2163044	0.91[ASN][1000 genomes]
rs2309650	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309729	0.83[ASN][1000 genomes]
rs2871316	0.86[ASN][1000 genomes]
rs34116173	0.93[ASN][1000 genomes]
rs34369751	0.93[ASN][1000 genomes]
rs3863005	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3863006	0.98[ASN][1000 genomes]
rs3915083	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4332968	0.89[ASN][1000 genomes]
rs4850914	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851225	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851226	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851228	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851229	0.98[ASN][1000 genomes]
rs4851230	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851231	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4851232	0.86[ASN][1000 genomes]
rs4851234	0.89[ASN][1000 genomes]
rs62147565	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6542890	0.98[ASN][1000 genomes]
rs6542891	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6705966	0.91[ASN][1000 genomes]
rs6708339	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6721652	0.93[ASN][1000 genomes]
rs6732358	0.91[ASN][1000 genomes]
rs6739478	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739601	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741990	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6744510	0.93[ASN][1000 genomes]
rs6746146	0.89[ASN][1000 genomes]
rs6748557	0.89[ASN][1000 genomes]
rs6756009	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6756821	0.93[ASN][1000 genomes]
rs6757262	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6758027	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558575	0.81[AMR][1000 genomes]
rs7559975	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561009	0.84[ASN][1000 genomes]
rs7562121	0.80[EUR][1000 genomes]
rs7565155	0.91[ASN][1000 genomes]
rs7573572	0.87[ASN][1000 genomes]
rs7582469	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7584365	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7589376	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7602699	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7604536	0.91[ASN][1000 genomes]
rs868665	0.86[ASN][1000 genomes]
rs9308829	0.91[ASN][1000 genomes]
rs940458	0.86[ASN][1000 genomes]
rs9967704	0.85[AMR][1000 genomes];0.98[EUR][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
rs2309690	IL1RL1	cis	cerebellum	SCAN
rs2309690	NFXL1	trans	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100346200-100379400	Weak transcription	Fetal Lung	lung
2	chr2:100357600-100389400	Weak transcription	Thymus	Thymus
3	chr2:100358400-100375400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr2:100358800-100375600	Strong transcription	Primary B cells from cord blood	blood
5	chr2:100359600-100379200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:100360000-100383400	Weak transcription	Ovary	ovary
7	chr2:100360000-100394600	Weak transcription	Dnd41	blood
8	chr2:100360200-100385200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:100365200-100379600	Weak transcription	Primary T cells from cord blood	blood
10	chr2:100367800-100386400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:100370000-100374600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:100372000-100373800	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr2:100372800-100374400	Enhancers	Lung	lung
14	chr2:100373200-100374600	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr2:100373200-100386000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:100373400-100373800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:100373600-100373800	Enhancers	Spleen	Spleen

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