Variant report

Variant	rs1719250
Chromosome Location	chr15:45609773-45609774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45607824..45610006-chr15:45694402..45696764,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171766	Chromatin interaction
ENSG00000171763	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1049508	0.83[MEX][hapmap]
rs1049518	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[MEX][hapmap]
rs10519018	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs10519022	0.83[MEX][hapmap]
rs1060896	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1145076	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs1145077	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs1145086	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1145089	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1145091	0.83[MEX][hapmap]
rs1145093	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1153845	0.91[MEX][hapmap]
rs1153858	0.83[MEX][hapmap]
rs1153860	0.80[EUR][1000 genomes]
rs1153862	0.82[ASN][1000 genomes]
rs11631021	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11632419	0.83[EUR][1000 genomes]
rs11632752	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11632778	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11632920	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11636114	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637364	0.83[EUR][1000 genomes]
rs11637838	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11637920	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11639349	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11639420	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11639483	0.80[AMR][1000 genomes]
rs11854365	0.83[EUR][1000 genomes]
rs11855414	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12437840	0.87[MEX][hapmap]
rs12437887	0.87[MEX][hapmap]
rs12440038	0.87[MEX][hapmap]
rs12440356	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12904150	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs12908818	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs12909409	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910009	0.83[EUR][1000 genomes]
rs12910764	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911186	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12915314	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1346266	0.82[MEX][hapmap]
rs1346267	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs1346268	0.87[MEX][hapmap]
rs1365610	0.87[MEX][hapmap]
rs1554521	0.87[MEX][hapmap]
rs1617634	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1617984	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1706767	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1706768	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1706770	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1706798	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1706829	1.00[CHD][hapmap]
rs1719231	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1719232	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1719236	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1719245	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1719246	0.91[CEU][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1719247	0.83[MEX][hapmap]
rs17536527	1.00[CHB][hapmap]
rs1820518	0.87[MEX][hapmap]
rs2002035	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015295	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271438	0.83[EUR][1000 genomes]
rs2413768	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2413771	0.80[EUR][1000 genomes]
rs2413772	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs2413774	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs2453533	0.80[EUR][1000 genomes]
rs2458225	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2461700	0.80[EUR][1000 genomes]
rs2461705	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2467853	0.91[CEU][hapmap]
rs2467865	0.80[EUR][1000 genomes]
rs2486274	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2687511	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2899375	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35861938	0.80[EUR][1000 genomes]
rs3759899	0.87[MEX][hapmap]
rs3809472	0.87[MEX][hapmap]
rs4395020	0.87[MEX][hapmap]
rs4774580	0.87[MEX][hapmap]
rs4775911	0.87[MEX][hapmap]
rs6493143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6493144	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6493145	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7164602	0.87[MEX][hapmap]
rs7165039	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7166580	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7167146	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs7171312	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8024620	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs8025079	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039138	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8039153	0.83[EUR][1000 genomes]
rs8039352	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8039354	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs8039540	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8041702	0.81[AMR][1000 genomes]
rs8042434	0.81[EUR][1000 genomes]
rs8043055	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs872192	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9921008	0.95[EUR][1000 genomes];0.89[ASN][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	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

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1719250	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs1719250	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs1719250	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs1719250	SLC28A2	cis	cerebellum	SCAN
rs1719250	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx
rs1719250	C15orf63	cis	parietal	SCAN
rs1719250	SPATA5L1	cis	multi-tissue	Pritchard
rs1719250	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs1719250	GATM	cis	parietal	SCAN
rs1719250	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs1719250	CTD-2651B20.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1719250	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs1719250	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs1719250	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs1719250	CTD-2651B20.3	cis	Thyroid	GTEx
rs1719250	CTD-2651B20.3	cis	Artery Aorta	GTEx
rs1719250	GATM	cis	cerebellum	SCAN
rs1719250	CTD-2651B20.3	cis	lung	GTEx
rs1719250	GATM	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45599600-45611000	Weak transcription	Right Atrium	heart
2	chr15:45603000-45611600	Weak transcription	Pancreas	Pancrea
3	chr15:45603200-45611600	Weak transcription	Rectal Mucosa Donor 31	rectum

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