Variant report

Variant	rs2002035
Chromosome Location	chr15:45613749-45613750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GATM-3	chr15:45613275-45613890	NONHSAT042234

Extended variants
information (count: 66 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1049518	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1145076	0.86[AMR][1000 genomes]
rs1145077	0.86[AMR][1000 genomes]
rs1145080	0.86[AMR][1000 genomes]
rs1145084	0.86[AMR][1000 genomes]
rs1145086	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1145089	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1145093	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1145097	0.88[AMR][1000 genomes]
rs1153855	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1153857	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1153860	0.88[AMR][1000 genomes]
rs1153862	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11631021	0.80[EUR][1000 genomes]
rs11636114	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11637364	0.80[EUR][1000 genomes]
rs11639349	0.80[EUR][1000 genomes]
rs11855414	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12440356	0.80[EUR][1000 genomes]
rs12908818	0.80[EUR][1000 genomes]
rs12909409	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910009	0.80[EUR][1000 genomes]
rs12910764	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1346267	0.86[AMR][1000 genomes]
rs1426932	0.86[AMR][1000 genomes]
rs1617634	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617984	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706767	0.80[EUR][1000 genomes]
rs1706768	0.80[EUR][1000 genomes]
rs1706770	0.80[EUR][1000 genomes]
rs1706798	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1719232	0.80[EUR][1000 genomes]
rs1719236	0.80[EUR][1000 genomes]
rs1719245	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719246	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1719250	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015295	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433601	0.85[AMR][1000 genomes]
rs2453533	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2458225	0.80[EUR][1000 genomes]
rs2461700	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2461705	0.80[EUR][1000 genomes]
rs2467853	0.86[AMR][1000 genomes]
rs2467862	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2467865	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2486274	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2486288	0.86[AMR][1000 genomes]
rs2687511	0.80[EUR][1000 genomes]
rs2899375	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35861938	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6493143	0.80[EUR][1000 genomes]
rs6493144	0.80[EUR][1000 genomes]
rs6493145	0.80[EUR][1000 genomes]
rs7166580	0.80[EUR][1000 genomes]
rs8024620	0.80[EUR][1000 genomes]
rs8025079	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8043055	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs872192	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921008	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv977713	chr15:45611707-45620772	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2002035	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs2002035	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs2002035	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2002035	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2002035	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs2002035	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs2002035	CTD-2651B20.3	cis	lung	GTEx
rs2002035	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2002035	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2002035	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs2002035	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs2002035	CTD-2651B20.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2002035	CTD-2651B20.3	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45612000-45615600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:45612400-45615600	Weak transcription	Gastric	stomach
3	chr15:45613000-45615600	Weak transcription	Stomach Mucosa	stomach
4	chr15:45613400-45613800	Enhancers	Fetal Brain Male	brain
5	chr15:45613400-45614000	Weak transcription	Fetal Brain Female	brain
6	chr15:45613600-45622000	Weak transcription	Pancreas	Pancrea

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