Variant report

Variant	rs40250
Chromosome Location	chr8:90841007-90841008
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	POLR2A	chr8:90840368-90841586	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:90800222..90801982-chr8:90840675..90842723,2	MCF-7	breast:
2	chr8:90838578..90843611-chr8:90912392..90915640,4	MCF-7	breast:
3	chr8:90838136..90841638-chr8:90842560..90845111,3	K562	blood:

Variant related genes	Relation type
COX6B1P6	TF binding region
ENSG00000207359	Chromatin interaction
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1003843	1.00[YRI][hapmap]
rs2189025	0.80[ASN][1000 genomes]
rs366867	0.89[ASN][1000 genomes]
rs367640	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs370282	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs374957	0.91[EUR][1000 genomes]
rs376962	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs377897	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs379015	0.93[ASN][1000 genomes]
rs380425	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs381456	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs386587	0.93[ASN][1000 genomes]
rs388866	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs390536	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs39500	1.00[YRI][hapmap]
rs39509	1.00[YRI][hapmap]
rs39519	0.93[EUR][1000 genomes]
rs39761	1.00[YRI][hapmap]
rs39771	0.94[EUR][1000 genomes]
rs39772	0.93[EUR][1000 genomes]
rs40247	1.00[YRI][hapmap]
rs402886	1.00[YRI][hapmap]
rs40382	0.83[ASN][1000 genomes]
rs40452	1.00[YRI][hapmap]
rs40453	1.00[YRI][hapmap]
rs40459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40547	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs40638	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs410663	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs411279	1.00[YRI][hapmap]
rs416324	1.00[YRI][hapmap]
rs418634	0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs419890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42186	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42346	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs42481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs425140	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs425312	0.92[EUR][1000 genomes]
rs426240	0.93[EUR][1000 genomes]
rs427854	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs43134	1.00[YRI][hapmap]
rs43135	0.83[ASN][1000 genomes]
rs43136	0.94[EUR][1000 genomes]
rs43225	1.00[YRI][hapmap]
rs43229	0.94[EUR][1000 genomes]
rs432457	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs438485	0.91[EUR][1000 genomes]
rs447618	1.00[YRI][hapmap]
rs447989	0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.94[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	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv968495	chr8:90835687-90842298	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2761448	chr8:90837630-90853986	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs40250	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90828000-90845800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:90837000-90847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr8:90837200-90844600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr8:90838800-90841200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:90839200-90848400	Weak transcription	Osteobl	bone
6	chr8:90840000-90846000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:90840000-90847400	Weak transcription	A549	lung
8	chr8:90841000-90841200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:90841000-90845800	Weak transcription	NHDF-Ad	bronchial

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