Variant report

Variant	rs890416
Chromosome Location	chr11:4493334-4493335
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10768026	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10836102	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032345	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032351	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032354	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032355	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032359	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11032361	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11032378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11032381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11032407	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12226120	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12788189	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1292642	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1864498	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1864499	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs189118	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs193063	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278170	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278171	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278172	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278173	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2554944	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2566264	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2915038	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs331503	0.96[CEU][hapmap];0.93[GIH][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs331523	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331524	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs331525	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs331526	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs331527	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs331529	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331530	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331531	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331532	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331533	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331534	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35390334	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55940502	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs890417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs890418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9633900	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9633905	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9633906	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1814887	chr11:4221216-4510188	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv427881	chr11:4221216-4510188	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv932141	chr11:4326065-4531854	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv896908	chr11:4367196-4552102	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1043803	chr11:4388448-4837042	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv540916	chr11:4388448-4837042	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
10	nsv553159	chr11:4389110-4599221	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1048224	chr11:4390227-4920324	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
12	nsv540917	chr11:4390227-4920324	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
13	nsv896911	chr11:4400801-4806872	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
14	nsv553160	chr11:4404192-4589567	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv553161	chr11:4404192-4589780	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1040278	chr11:4440162-4530349	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv1039640	chr11:4476167-4541813	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv521561	chr11:4476699-4536230	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv523709	chr11:4476699-4540077	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv1038290	chr11:4491101-4530349	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs890416	OSBPL5	cis	cerebellum	SCAN
rs890416	OR52K2	cis	multi-tissue	Pritchard
rs890416	C11orf21	cis	parietal	SCAN
rs890416	MUC2	cis	parietal	SCAN
rs890416	OR51I2	cis	parietal	SCAN
rs890416	OR52K3P	cis	Whole Blood	GTEx
rs890416	KRTAP5-5	cis	parietal	SCAN
rs890416	IGF2AS	cis	cerebellum	SCAN
rs890416	OR52L1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4488000-4496000	Weak transcription	Gastric	stomach
2	chr11:4488600-4501800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:4493000-4495600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr11:4493000-4495800	Weak transcription	Monocytes-CD14+_RO01746	blood

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