Variant report

Variant	rs10507575
Chromosome Location	chr13:53791404-53791405
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	chr13:53225145..53227561-chr13:53790469..53792639,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165416	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs12860364	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12865218	0.83[EUR][1000 genomes]
rs12867491	0.86[EUR][1000 genomes]
rs12869523	0.86[EUR][1000 genomes]
rs12870777	0.86[EUR][1000 genomes]
rs12871248	0.86[EUR][1000 genomes]
rs12874939	0.86[EUR][1000 genomes]
rs12876105	0.86[EUR][1000 genomes]
rs12876387	0.83[EUR][1000 genomes]
rs12876786	0.89[EUR][1000 genomes]
rs12877178	0.83[EUR][1000 genomes]
rs12877599	0.86[EUR][1000 genomes]
rs12877758	0.86[EUR][1000 genomes]
rs12877912	0.89[EUR][1000 genomes]
rs1322946	0.96[ASN][1000 genomes]
rs1343608	0.86[EUR][1000 genomes]
rs1555549	0.90[ASN][1000 genomes]
rs17053814	0.90[TSI][hapmap]
rs17054812	0.86[EUR][1000 genomes]
rs17054937	0.89[EUR][1000 genomes]
rs1909651	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275840	0.90[TSI][hapmap]
rs2806957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34030659	0.86[EUR][1000 genomes]
rs34031649	0.86[EUR][1000 genomes]
rs34059997	0.86[EUR][1000 genomes]
rs34163916	0.83[EUR][1000 genomes]
rs34201111	0.86[EUR][1000 genomes]
rs34211399	0.83[EUR][1000 genomes]
rs34298498	0.83[EUR][1000 genomes]
rs34330988	0.83[EUR][1000 genomes]
rs34531708	0.86[EUR][1000 genomes]
rs34557321	0.89[EUR][1000 genomes]
rs34642277	0.83[EUR][1000 genomes]
rs34687272	0.86[EUR][1000 genomes]
rs34708622	0.83[EUR][1000 genomes]
rs34756826	0.84[EUR][1000 genomes]
rs34902019	0.86[EUR][1000 genomes]
rs35003538	0.83[EUR][1000 genomes]
rs35007240	0.83[EUR][1000 genomes]
rs35114755	0.86[EUR][1000 genomes]
rs35226075	0.83[EUR][1000 genomes]
rs35340650	0.89[EUR][1000 genomes]
rs35575822	0.83[EUR][1000 genomes]
rs35625606	0.83[EUR][1000 genomes]
rs35628629	0.86[EUR][1000 genomes]
rs35666947	0.83[EUR][1000 genomes]
rs35727089	0.83[EUR][1000 genomes]
rs35756659	0.83[EUR][1000 genomes]
rs35765587	0.83[EUR][1000 genomes]
rs35800707	0.89[EUR][1000 genomes]
rs36044845	1.00[AFR][1000 genomes]
rs55702516	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55972529	0.86[EUR][1000 genomes]
rs57273256	0.86[EUR][1000 genomes]
rs57454139	0.83[EUR][1000 genomes]
rs59297590	0.86[EUR][1000 genomes]
rs59486247	0.94[EUR][1000 genomes]
rs59513810	0.83[EUR][1000 genomes]
rs59960345	0.86[EUR][1000 genomes]
rs60408242	0.86[EUR][1000 genomes]
rs61950074	0.83[EUR][1000 genomes]
rs61950079	0.86[EUR][1000 genomes]
rs61950086	0.86[EUR][1000 genomes]
rs61950134	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61950504	0.83[EUR][1000 genomes]
rs61950522	0.83[EUR][1000 genomes]
rs6561705	0.81[EUR][1000 genomes]
rs6561706	0.86[EUR][1000 genomes]
rs6561707	0.86[EUR][1000 genomes]
rs7320513	0.86[EUR][1000 genomes]
rs7325509	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74086489	0.83[EUR][1000 genomes]
rs7998204	0.86[EUR][1000 genomes]
rs7998385	0.94[EUR][1000 genomes]
rs8002469	0.82[MEX][hapmap];0.90[TSI][hapmap]
rs912053	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9563134	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9563136	0.89[EUR][1000 genomes]
rs9563137	0.89[EUR][1000 genomes]
rs9563138	0.89[EUR][1000 genomes]
rs9563145	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9563146	0.84[ASN][1000 genomes]
rs9563147	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568814	0.89[EUR][1000 genomes]
rs9568815	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9568816	0.89[EUR][1000 genomes]
rs9568817	0.89[EUR][1000 genomes]
rs9568820	0.89[EUR][1000 genomes]
rs9568821	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9568822	0.89[EUR][1000 genomes]
rs9568823	0.89[EUR][1000 genomes]
rs9568824	0.89[EUR][1000 genomes]
rs9568825	0.89[EUR][1000 genomes]
rs9568827	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568828	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9568834	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs995821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1050969	chr13:53665927-54064861	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1840677	chr13:53774627-53791895	Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10507575	SUGT1	cis	brain	seeQTL
rs10507575	IL13	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53790800-53791600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr13:53791400-53792400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:53791400-53792400	Enhancers	Pancreatic Islets	Pancreatic Islet

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