Variant report

Variant	rs1320391
Chromosome Location	chr11:87309908-87309909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1010308	0.89[ASN][1000 genomes]
rs10751167	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10751168	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs10751169	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs10751173	0.82[EUR][1000 genomes]
rs10751174	0.82[EUR][1000 genomes]
rs10792969	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792972	0.81[EUR][1000 genomes]
rs10898726	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10898738	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898740	0.88[ASN][1000 genomes]
rs10898741	0.88[ASN][1000 genomes]
rs10898749	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10898751	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11235216	0.89[ASN][1000 genomes]
rs11235217	0.87[ASN][1000 genomes]
rs11235218	0.88[ASN][1000 genomes]
rs11235219	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11235220	0.88[ASN][1000 genomes]
rs11235222	0.83[ASN][1000 genomes]
rs11235223	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11235238	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12288923	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12295687	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2000797	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2019620	0.89[ASN][1000 genomes]
rs2097037	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2097039	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097040	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2156452	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2156455	0.89[ASN][1000 genomes]
rs2187329	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2212951	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2212955	0.81[ASN][1000 genomes]
rs2226840	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2226842	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2375043	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3892758	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3924408	0.89[ASN][1000 genomes]
rs4084199	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4463863	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4517548	0.81[ASN][1000 genomes]
rs4641509	0.82[EUR][1000 genomes]
rs4943988	0.89[ASN][1000 genomes]
rs4944727	0.88[ASN][1000 genomes]
rs4944729	0.88[ASN][1000 genomes]
rs4944731	0.84[ASN][1000 genomes]
rs4944745	0.83[EUR][1000 genomes]
rs4944746	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6592388	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592396	0.91[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs7127034	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7127893	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7924703	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs940238	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv555714	chr11:87058981-87399218	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1039172	chr11:87068731-87385458	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv832224	chr11:87162121-87355923	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv898075	chr11:87278074-87375119	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
7	esv2760195	chr11:87295119-87329156	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv555715	chr11:87307553-87349407	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1320391	NAALAD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:87296400-87313600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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