Variant report

Variant	rs2415209
Chromosome Location	chr15:73262691-73262692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73261869..73264413-chr15:73266352..73269682,3	MCF-7	breast:
2	chr15:73262265..73265047-chr15:73342979..73345241,3	MCF-7	breast:
3	chr15:73258951..73261600-chr15:73262517..73265524,3	MCF-7	breast:
4	chr15:73262584..73265850-chr15:73343191..73346081,4	MCF-7	breast:
5	chr15:73234817..73236569-chr15:73261756..73264144,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1080331	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1080332	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072398	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072401	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11632783	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11639220	0.99[ASN][1000 genomes]
rs12438940	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440392	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441946	0.86[JPT][hapmap]
rs12442084	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12443302	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12592939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12594272	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901593	0.97[ASN][1000 genomes]
rs1375496	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449267	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1449269	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs1449270	0.87[ASN][1000 genomes]
rs1466111	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1823338	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1839270	0.86[JPT][hapmap]
rs1839271	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1900901	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979106	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2053857	0.80[ASN][1000 genomes]
rs2122217	0.90[ASN][1000 genomes]
rs2415212	0.81[ASN][1000 genomes]
rs2415213	0.81[ASN][1000 genomes]
rs28424084	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28451690	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28513521	0.98[ASN][1000 genomes]
rs28615518	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28647826	0.99[ASN][1000 genomes]
rs28653293	0.81[EUR][1000 genomes]
rs28666516	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28686814	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34173815	0.80[ASN][1000 genomes]
rs4076146	0.99[ASN][1000 genomes]
rs4238456	0.84[ASN][1000 genomes]
rs4238457	0.84[ASN][1000 genomes]
rs4238458	0.84[ASN][1000 genomes]
rs4260029	0.84[ASN][1000 genomes]
rs4260030	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4286085	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4297657	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4328412	0.84[ASN][1000 genomes]
rs4360901	0.97[ASN][1000 genomes]
rs4366688	0.97[ASN][1000 genomes]
rs4374145	0.97[ASN][1000 genomes]
rs4383117	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4401026	0.88[ASN][1000 genomes]
rs4430712	0.80[ASN][1000 genomes]
rs4468585	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4511500	0.88[ASN][1000 genomes]
rs4522396	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4531709	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4563021	0.84[ASN][1000 genomes]
rs4572358	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4575500	0.84[ASN][1000 genomes]
rs4597288	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4777569	0.80[ASN][1000 genomes]
rs4777577	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4777578	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55768020	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60053960	0.90[ASN][1000 genomes]
rs60557800	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62015256	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495033	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495035	0.86[ASN][1000 genomes]
rs6495036	0.89[ASN][1000 genomes]
rs6495037	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495038	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495039	0.97[ASN][1000 genomes]
rs6495040	0.97[ASN][1000 genomes]
rs6495042	0.86[ASN][1000 genomes]
rs7164304	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164592	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165104	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165325	0.97[ASN][1000 genomes]
rs7165504	0.97[ASN][1000 genomes]
rs7165834	0.88[ASN][1000 genomes]
rs7166470	0.97[ASN][1000 genomes]
rs7178831	0.99[ASN][1000 genomes]
rs7180332	0.99[ASN][1000 genomes]
rs7183175	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7496513	0.86[ASN][1000 genomes]
rs8025463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025665	0.83[ASW][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8031589	0.84[ASN][1000 genomes]
rs8033793	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033860	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033954	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034120	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8036013	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921261	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521475	chr15:73250485-73263405	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2415209	NEO1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73254800-73263200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:73258000-73264400	Enhancers	Fetal Brain Male	brain
3	chr15:73259200-73263400	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr15:73260400-73262800	Weak transcription	Fetal Stomach	stomach
5	chr15:73260400-73263600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:73260400-73263800	Weak transcription	Colonic Mucosa	Colon
7	chr15:73261200-73263200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:73261200-73263400	Weak transcription	Right Atrium	heart
9	chr15:73261400-73263200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:73261400-73263400	Weak transcription	Fetal Intestine Large	intestine
11	chr15:73261400-73263400	Weak transcription	Fetal Intestine Small	intestine
12	chr15:73261400-73263600	Weak transcription	Fetal Heart	heart
13	chr15:73261400-73263600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:73261600-73262800	Weak transcription	Fetal Lung	lung
15	chr15:73261600-73263000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:73261600-73263000	Weak transcription	Fetal Kidney	kidney
17	chr15:73262000-73263200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:73262200-73265000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:73262400-73263800	Enhancers	Fetal Brain Female	brain
20	chr15:73262600-73263000	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:73262600-73263000	Weak transcription	Psoas Muscle	Psoas
22	chr15:73262600-73263400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:73262600-73263400	Weak transcription	Spleen	Spleen

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