Variant report

Variant	rs1561714
Chromosome Location	chr8:96119975-96119976
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:96118492..96120105-chr8:96144692..96147118,2	MCF-7	breast:
2	chr8:96112153..96114235-chr8:96119787..96121888,2	MCF-7	breast:
3	chr8:96119610..96121768-chr8:96178748..96180708,2	MCF-7	breast:
4	chr8:96112179..96116026-chr8:96118570..96123385,6	K562	blood:
5	chr8:96119972..96121573-chr8:96125968..96128452,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156170	Chromatin interaction
ENSG00000175895	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10102994	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10808672	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11781181	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466169	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1561715	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs172469	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1975425	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2044034	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2583365	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2599726	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2678841	0.84[CEU][hapmap]
rs297550	0.89[CEU][hapmap]
rs297557	0.84[AMR][1000 genomes]
rs4392868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4735344	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4735345	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4735346	0.81[EUR][1000 genomes]
rs4735347	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4735350	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56617377	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6471516	0.84[CEU][hapmap]
rs6983365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6987741	0.96[EUR][1000 genomes]
rs7000568	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7000734	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7002233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs732280	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7822998	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7836804	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7845016	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv891207	chr8:96106037-96160914	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1561714	TSPYL5	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96113800-96122400	Weak transcription	Gastric	stomach
2	chr8:96113800-96122400	Weak transcription	Pancreas	Pancrea
3	chr8:96113800-96127800	Weak transcription	Right Ventricle	heart
4	chr8:96115600-96122400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:96115600-96122600	Weak transcription	Osteobl	bone
6	chr8:96115800-96123200	Weak transcription	K562	blood
7	chr8:96116200-96121800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:96117600-96122400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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