Variant report

Variant	rs1999716
Chromosome Location	chr13:29813633-29813634
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC7A1-2	chr13:29813516-29814095	ENSG00000236758.1
2	lnc-SLC7A1-2	chr13:29813496-29813733	NONHSAT032720

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1111373	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1335655	1.00[CEU][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1335662	0.92[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1577477	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1927830	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs1927833	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[MEX][hapmap]
rs2182989	0.80[EUR][1000 genomes]
rs3932642	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4769687	0.85[CEU][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes]
rs4769691	0.83[CEU][hapmap]
rs4769697	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56332852	0.82[EUR][1000 genomes]
rs7987149	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7992989	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997471	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9508311	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9551608	0.84[CEU][hapmap]
rs9551612	0.84[CEU][hapmap]
rs9551615	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9579304	0.85[CEU][hapmap]
rs989845	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs989846	0.85[CEU][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533835	chr13:29141132-29962069	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3406145	chr13:29616606-29917459	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899957	chr13:29720732-29820422	Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv427927	chr13:29729315-30062054	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv899958	chr13:29752497-29820422	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv899959	chr13:29752497-29832613	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3433497	chr13:29786122-29917797	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3347671	chr13:29786276-29922806	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3371345	chr13:29786316-29922762	Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1999716	KCNH1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:29807800-29820400	Weak transcription	Aorta	Aorta
2	chr13:29811600-29815200	Weak transcription	Fetal Thymus	thymus
3	chr13:29813400-29814600	Enhancers	Primary T cells from cord blood	blood
4	chr13:29813600-29815000	Flanking Active TSS	Dnd41	blood

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