Variant report

Variant	rs2339109
Chromosome Location	chr8:91241247-91241248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:91228314..91231823-chr8:91238061..91241526,6	K562	blood:
2	chr8:91240676..91242950-chr8:91249101..91250668,2	MCF-7	breast:
3	chr8:90913953..90916622-chr8:91239898..91242343,2	K562	blood:
4	chr8:91196894..91200069-chr8:91240130..91243292,3	K562	blood:
5	chr8:91227850..91231823-chr8:91238006..91241292,4	K562	blood:

Variant related genes	Relation type
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10086980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10096924	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12676897	0.85[EUR][1000 genomes]
rs12679473	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12679936	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12681301	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12682044	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13253603	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13275049	0.98[ASN][1000 genomes]
rs13276534	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13439055	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16904163	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056839	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2056840	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2158222	1.00[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189258	0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2339108	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28465357	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2879344	0.87[EUR][1000 genomes]
rs33958462	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62530359	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67438267	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7823556	0.86[LWK][hapmap]
rs7842660	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9642892	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9643256	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9643257	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968950	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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	esv2758164	chr8:91000786-91329669	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2759628	chr8:91000786-91329669	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2339109	RUNX1T1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:91240000-91242000	Genic enhancers	K562	blood
2	chr8:91240200-91244200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:91240600-91244800	Enhancers	Hela-S3	cervix
4	chr8:91241000-91241400	Enhancers	HMEC	breast
5	chr8:91241200-91241400	Enhancers	NHEK	skin
6	chr8:91241200-91243400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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