Variant report

Variant	rs12620982
Chromosome Location	chr2:100238379-100238380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10167554	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123790	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11684088	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712049	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712054	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13029690	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1357719	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996984	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2030691	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2030692	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2030693	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2049400	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2177541	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177542	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792129	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3792130	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792131	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850910	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4851220	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4851221	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6542884	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6738724	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6745568	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7579222	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9284724	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308826	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9308827	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9678859	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12620982	IL1RL1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100211000-100249600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:100217000-100258400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:100218200-100241400	Weak transcription	Spleen	Spleen
4	chr2:100224800-100239800	Weak transcription	Right Ventricle	heart
5	chr2:100231000-100240400	Weak transcription	Fetal Kidney	kidney
6	chr2:100231200-100238600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:100231400-100243400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:100232400-100238600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:100232400-100242800	Weak transcription	Lung	lung
10	chr2:100234400-100243200	Enhancers	Fetal Brain Male	brain
11	chr2:100235800-100243800	Strong transcription	Primary B cells from cord blood	blood
12	chr2:100236200-100240000	Weak transcription	Fetal Heart	heart
13	chr2:100236200-100241000	Weak transcription	Adipose Nuclei	Adipose
14	chr2:100236400-100241400	Enhancers	Stomach Smooth Muscle	stomach
15	chr2:100236600-100240000	Weak transcription	Gastric	stomach
16	chr2:100236800-100249600	Weak transcription	Thymus	Thymus
17	chr2:100237000-100239600	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:100237000-100239600	Enhancers	HSMMtube	muscle
19	chr2:100237000-100241600	Weak transcription	Fetal Intestine Small	intestine
20	chr2:100237200-100238400	Enhancers	Fetal Muscle Leg	muscle
21	chr2:100237400-100240600	Enhancers	Colon Smooth Muscle	Colon
22	chr2:100237600-100238600	Weak transcription	Fetal Brain Female	brain
23	chr2:100237800-100238800	Enhancers	Fetal Lung	lung
24	chr2:100237800-100240000	Weak transcription	Right Atrium	heart
25	chr2:100237800-100249400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:100238000-100238400	Weak transcription	Fetal Stomach	stomach
27	chr2:100238000-100239800	Weak transcription	Left Ventricle	heart
28	chr2:100238000-100253200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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