Variant report

Variant	rs11690399
Chromosome Location	chr2:113740259-113740260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL36G-1	chr2:113739523-113741050	ucscGeneNc_uc002tjs_2

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10178396	0.85[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10188477	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10188765	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10206205	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10221977	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10864908	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11123153	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11123154	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11674086	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11676013	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs11897907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13029531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13029703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13030063	0.85[YRI][hapmap]
rs1562305	0.89[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1867827	0.96[ASN][1000 genomes]
rs1867828	0.97[ASN][1000 genomes]
rs2305151	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4254516	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849142	0.85[YRI][hapmap]
rs58593758	0.99[ASN][1000 genomes]
rs6710007	0.85[YRI][hapmap]
rs6744288	1.00[YRI][hapmap]
rs6747618	0.85[CEU][hapmap];0.90[GIH][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7559466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7578034	0.93[ASN][1000 genomes]
rs7580877	0.96[ASN][1000 genomes]
rs879710	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs879711	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS 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	12 gene(s)	inside rSNPs	diseases
5	nsv961489	chr2:113737947-113742104	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11690399	ACOXL	cis	parietal	SCAN
rs11690399	DPP10	cis	parietal	SCAN
rs11690399	IL1B	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113736000-113747400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113737400-113742400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:113737600-113742600	Weak transcription	Thymus	Thymus
4	chr2:113738400-113742000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:113738400-113742400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:113738400-113742400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:113738600-113742000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:113738600-113742200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:113738600-113742200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:113738600-113742400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:113739000-113742200	Weak transcription	Fetal Thymus	thymus
12	chr2:113739200-113742200	Weak transcription	Primary T cells from cord blood	blood
13	chr2:113739200-113742200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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