Variant report

Variant	rs2412395
Chromosome Location	chr11:4871036-4871037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:4869840-4870943..11:4870943-4872364	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000176922	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10500625	1.00[CEU][hapmap]
rs10500626	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs10500631	1.00[CEU][hapmap]
rs11034067	0.83[CEU][hapmap]
rs11034071	0.83[CEU][hapmap]
rs11034089	0.83[CEU][hapmap]
rs11034090	0.83[CEU][hapmap]
rs11034094	0.83[CEU][hapmap]
rs12785245	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs12785274	0.91[CEU][hapmap]
rs12786973	0.91[CEU][hapmap]
rs12787796	0.83[CEU][hapmap]
rs12788447	1.00[CEU][hapmap]
rs12793425	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12794894	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs12795212	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs12796015	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs12796618	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12799928	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12801339	0.82[AMR][1000 genomes]
rs12801368	0.91[CEU][hapmap]
rs12801465	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12802922	1.00[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs12804676	1.00[CEU][hapmap]
rs12806014	1.00[CEU][hapmap]
rs12806727	0.87[EUR][1000 genomes]
rs1433899	1.00[CEU][hapmap]
rs1541946	0.83[CEU][hapmap]
rs17227456	0.82[AMR][1000 genomes]
rs17227484	0.83[GIH][hapmap]
rs17228176	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs17228183	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs17228218	0.83[CEU][hapmap]
rs17247598	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs17249369	0.91[CEU][hapmap]
rs17249695	0.83[CEU][hapmap]
rs17250199	0.91[CEU][hapmap]
rs17251220	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17251261	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17327845	0.91[CEU][hapmap]
rs17327907	0.91[CEU][hapmap]
rs17328143	0.83[CEU][hapmap]
rs17328337	0.83[CEU][hapmap]
rs17328565	0.91[CEU][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17329242	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17337601	0.85[EUR][1000 genomes]
rs17337649	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs1865282	0.83[CEU][hapmap]
rs1897739	0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs34301246	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34583466	0.85[EUR][1000 genomes]
rs34742470	0.85[EUR][1000 genomes]
rs34885098	0.82[AMR][1000 genomes]
rs35408660	0.87[EUR][1000 genomes]
rs35720831	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35918613	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36060165	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4910686	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs4910687	0.83[CEU][hapmap]
rs4910688	0.82[CEU][hapmap]
rs4910691	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71480716	0.82[AMR][1000 genomes]
rs7925039	0.94[EUR][1000 genomes]
rs7948040	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv3424302	chr11:4585155-4880050	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	esv2760633	chr11:4803980-4910384	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1035355	chr11:4805922-4907672	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1039703	chr11:4806669-4910372	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv553176	chr11:4806706-4909000	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv553177	chr11:4806872-4871506	Enhancers Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv553178	chr11:4806872-4909000	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv553179	chr11:4806872-4910224	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1045537	chr11:4807304-4904064	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv467665	chr11:4808227-4871481	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv553180	chr11:4808227-4871481	Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv553181	chr11:4811933-4910224	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv553182	chr11:4814850-4909000	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv1035941	chr11:4815059-4904064	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv553183	chr11:4815348-4909000	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv467666	chr11:4815348-4917089	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv553184	chr11:4815348-4917089	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv553185	chr11:4816548-4905202	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
22	nsv553187	chr11:4819907-4883396	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv553188	chr11:4823783-4909000	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2412395	OR2D3	cis	parietal	SCAN
rs2412395	RPL27A	cis	cerebellum	SCAN
rs2412395	FXC1	cis	cerebellum	SCAN
rs2412395	LSP1	cis	parietal	SCAN
rs2412395	TSPAN4	cis	cerebellum	SCAN
rs2412395	OR51E2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4870400-4871600	Enhancers	Fetal Heart	heart
2	chr11:4870800-4872200	Weak transcription	Liver	Liver

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