Variant report

Variant	rs1669867
Chromosome Location	chr15:52746861-52746862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52746584..52749039-chr15:52819841..52822559,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1001522	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10083671	0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10083673	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1009157	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap]
rs10467925	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs10518687	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs10851519	0.84[YRI][hapmap]
rs1125460	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12324100	0.89[CEU][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs12324121	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs12898655	0.86[ASN][1000 genomes]
rs12909874	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12914979	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs1464963	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1464964	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1612233	0.84[YRI][hapmap]
rs1669856	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1669858	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1693490	0.84[LWK][hapmap];0.81[YRI][hapmap]
rs1693491	0.81[YRI][hapmap]
rs1724589	0.82[AFR][1000 genomes]
rs1724591	0.84[AFR][1000 genomes]
rs1724628	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1724629	0.89[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1724631	0.94[ASW][hapmap];0.84[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1724634	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1724639	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1724641	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17542017	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17613475	0.96[MEX][hapmap]
rs2242057	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs2242058	0.89[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs2414150	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2414151	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2444013	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2453987	0.84[YRI][hapmap]
rs2462845	0.80[YRI][hapmap]
rs2693464	0.83[YRI][hapmap]
rs2693471	0.81[YRI][hapmap]
rs2950056	0.88[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs35134548	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35523401	0.88[ASN][1000 genomes]
rs3858907	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4280181	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4519295	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4776046	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62023267	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176061	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7176482	0.89[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs7176639	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs7182150	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs722436	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs752864	0.90[CHB][hapmap]
rs752865	0.89[CEU][hapmap];0.91[CHB][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs752866	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs8028033	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs935892	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1669867	MYO5A	cis	cerebellum	SCAN
rs1669867	SPPL2A	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52732600-52750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:52734600-52753200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:52734800-52747400	Weak transcription	HSMM	muscle
4	chr15:52739000-52751800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:52739000-52753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:52740400-52756200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:52740600-52753200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr15:52742000-52755800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:52742200-52751600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:52742200-52753000	Weak transcription	NHEK	skin
11	chr15:52743800-52758200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:52744200-52747000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:52744600-52749200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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