Variant report

Variant	rs10993229
Chromosome Location	chr9:97286352-97286353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIATL1-12	chr9:97285819-97288385	NONHSAT133323

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10124212	0.86[AFR][1000 genomes]
rs10993225	0.88[AFR][1000 genomes]
rs2772018	0.88[AFR][1000 genomes]
rs2772019	0.88[AFR][1000 genomes]
rs2772020	0.88[AFR][1000 genomes]
rs2790405	0.88[AFR][1000 genomes]
rs2945800	0.85[AFR][1000 genomes]
rs2987892	0.84[AFR][1000 genomes]
rs2987893	0.88[AFR][1000 genomes]
rs2987894	0.88[AFR][1000 genomes]
rs2987895	0.80[AFR][1000 genomes]
rs2993979	0.88[AFR][1000 genomes]
rs488622	0.83[AFR][1000 genomes]
rs493408	0.83[AFR][1000 genomes]
rs497103	0.83[AFR][1000 genomes]
rs497200	0.83[AFR][1000 genomes]
rs497949	0.82[AFR][1000 genomes]
rs57090717	0.88[AFR][1000 genomes]
rs573331	0.88[AFR][1000 genomes]
rs576240	0.88[AFR][1000 genomes]
rs591824	0.83[AFR][1000 genomes]
rs59289025	0.88[AFR][1000 genomes]
rs659013	0.86[AFR][1000 genomes]
rs687553	0.83[AFR][1000 genomes]
rs925932	0.85[AFR][1000 genomes]
rs9299425	0.88[AFR][1000 genomes]
rs9409576	0.87[AFR][1000 genomes]
rs9409578	0.88[AFR][1000 genomes]
rs9409796	0.87[AFR][1000 genomes]
rs9696782	0.88[AFR][1000 genomes]
rs9697257	0.86[AFR][1000 genomes]
rs9775007	0.81[AFR][1000 genomes]
rs9775017	0.86[AFR][1000 genomes]
rs9776527	0.88[AFR][1000 genomes]
rs9777599	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv969761	chr9:97254596-97288069	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv893595	chr9:97268182-97330693	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10993229	HIATL1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97278000-97295200	Weak transcription	Liver	Liver

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