Variant report

Variant	rs2413769
Chromosome Location	chr15:45561868-45561869
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:45561800-45561950	GM12869	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45560533..45562210-chr15:45570585..45573107,2	MCF-7	breast:

Variant related genes	Relation type
SLC28A2	TF binding region
ENSG00000259520	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10444821	0.93[JPT][hapmap]
rs1049508	0.93[JPT][hapmap];0.88[MEX][hapmap]
rs10519022	0.93[JPT][hapmap];0.88[MEX][hapmap]
rs1145091	0.93[JPT][hapmap];0.88[MEX][hapmap]
rs1153849	0.93[JPT][hapmap];0.84[MEX][hapmap]
rs1153858	0.93[JPT][hapmap];0.88[MEX][hapmap]
rs11855527	0.85[EUR][1000 genomes]
rs12437840	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs12437887	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs12440038	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs12593370	0.91[JPT][hapmap]
rs12593402	0.92[JPT][hapmap]
rs1288775	0.93[JPT][hapmap]
rs12901747	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909158	1.00[JPT][hapmap]
rs12910143	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913645	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346266	0.93[JPT][hapmap];0.87[MEX][hapmap]
rs1346268	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs1365610	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs1554521	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs1648302	0.92[JPT][hapmap]
rs16941017	0.92[JPT][hapmap]
rs1706770	0.80[YRI][hapmap]
rs1706772	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1706824	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719231	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719237	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719247	1.00[JPT][hapmap];0.88[MEX][hapmap]
rs1820518	0.93[JPT][hapmap];0.95[MEX][hapmap]
rs1980288	1.00[JPT][hapmap]
rs2056493	0.93[JPT][hapmap]
rs2066090	0.93[JPT][hapmap]
rs2413775	0.92[JPT][hapmap]
rs2433228	0.92[JPT][hapmap]
rs2433229	0.92[JPT][hapmap]
rs2467858	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs2687512	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759895	0.92[JPT][hapmap]
rs3759899	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs3809472	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs4395020	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs4627277	0.86[CEU][hapmap];0.92[JPT][hapmap]
rs4774550	0.92[JPT][hapmap]
rs4774580	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs4775911	0.93[JPT][hapmap];0.92[MEX][hapmap]
rs7164602	0.93[JPT][hapmap];0.96[MEX][hapmap]
rs8032904	0.93[JPT][hapmap]
rs8033629	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8039476	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs2413769	SPATA5L1	cis	Esophagus Muscularis	GTEx
rs2413769	CTD-2651B20.3	cis	Thyroid	GTEx
rs2413769	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2413769	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL
rs2413769	SPATA5L1	cis	Thyroid	GTEx
rs2413769	CTD-2651B20.3	cis	lung	GTEx
rs2413769	SPATA5L1	cis	Whole Blood	GTEx
rs2413769	TMEM87A	cis	parietal	SCAN
rs2413769	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs2413769	SPATA5L1	cis	multi-tissue	Pritchard
rs2413769	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2413769	GATM	cis	Muscle Skeletal	GTEx
rs2413769	GATM	cis	multi-tissue	Pritchard
rs2413769	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs2413769	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2413769	BMF	cis	parietal	SCAN
rs2413769	SPATA5L1	cis	parietal	SCAN
rs2413769	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs2413769	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs2413769	SPATA5L1	cis	Frontal Cortex	GTEx
rs2413769	GATM	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45550200-45570600	Weak transcription	Stomach Mucosa	stomach
2	chr15:45552600-45570600	Weak transcription	Pancreas	Pancrea
3	chr15:45553800-45569000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:45558000-45570400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:45560600-45566800	Weak transcription	Fetal Intestine Small	intestine
6	chr15:45560600-45570400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:45560600-45570600	Weak transcription	Fetal Stomach	stomach
8	chr15:45561200-45567600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr15:45561800-45562000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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