Variant report

Variant	rs7930102
Chromosome Location	chr11:57814759-57814760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR9I1-1	chr11:57814729-57815019	ENSG00000255146

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1031234	0.80[CEU][hapmap]
rs1113334	0.85[ASN][1000 genomes]
rs1113335	0.85[ASN][1000 genomes]
rs11600060	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs11601202	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11601223	0.87[ASN][1000 genomes]
rs11601663	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11601841	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs11604473	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs11604630	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs11605988	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11606464	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11607308	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608016	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12790525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792435	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12792638	0.87[ASN][1000 genomes]
rs12801976	0.85[ASN][1000 genomes]
rs12805812	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs1376489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17152364	0.89[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs17152376	0.92[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs1814059	0.92[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs1868881	0.94[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2089747	0.85[ASN][1000 genomes]
rs2441952	0.84[CEU][hapmap]
rs34015013	0.88[ASN][1000 genomes]
rs34300518	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35163247	0.88[ASN][1000 genomes]
rs35742790	0.88[ASN][1000 genomes]
rs36071925	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3853676	0.84[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs4509781	0.96[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61903966	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61903967	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61904009	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61904011	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61904024	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61905309	0.88[ASN][1000 genomes]
rs67305834	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7113760	0.96[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7117205	0.90[LWK][hapmap]
rs7120102	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs7120442	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs7121128	0.85[ASN][1000 genomes]
rs7123727	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7929515	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7934149	0.84[AMR][1000 genomes]
rs7934184	0.92[CEU][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs7935428	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap]
rs7936998	0.90[LWK][hapmap]
rs7938062	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs7945154	0.90[CEU][hapmap];0.89[JPT][hapmap]
rs7949558	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs930703	0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7930102	DDB1	cis	cerebellum	SCAN
rs7930102	UBE2L6	cis	parietal	SCAN
rs7930102	OR5M10	cis	parietal	SCAN
rs7930102	OR5M1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57813600-57825000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:57814400-57815200	Enhancers	HepG2	liver

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