Variant report

Variant	rs9987281
Chromosome Location	chr8:86348830-86348831
allele	A/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	FOS	chr8:86348622-86348856	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr8:86348564-86348893	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr8:86348567-86348856	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr8:86348566-86348891	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:86348746..86351284-chr8:86374911..86377490,2	MCF-7	breast:

Variant related genes	Relation type
CA3	TF binding region
ENSG00000104267	Chromatin interaction
ENSG00000253549	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10087278	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10091566	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10095352	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10097917	0.83[ASN][1000 genomes]
rs10111039	0.82[ASN][1000 genomes]
rs10504812	0.95[JPT][hapmap]
rs10504813	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10907474	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs11261471	0.86[JPT][hapmap]
rs11261474	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11985029	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11985733	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12541445	0.86[JPT][hapmap]
rs12543256	0.82[JPT][hapmap]
rs12544332	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12546106	0.82[JPT][hapmap]
rs12550814	0.91[ASN][1000 genomes]
rs1303806	0.95[JPT][hapmap]
rs13252971	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13255540	0.85[ASN][1000 genomes]
rs13259399	0.91[JPT][hapmap]
rs13273654	0.88[ASN][1000 genomes]
rs1389245	0.84[ASN][1000 genomes]
rs1389247	0.84[ASN][1000 genomes]
rs1390711	0.95[JPT][hapmap]
rs1390712	0.95[ASN][1000 genomes]
rs1493302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1496529	1.00[JPT][hapmap]
rs1496530	1.00[JPT][hapmap]
rs1496531	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1496532	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1532423	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1532424	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1543852	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1553015	0.95[JPT][hapmap]
rs16913721	0.91[JPT][hapmap]
rs17042	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs17740658	0.82[JPT][hapmap]
rs1908075	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995056	0.90[JPT][hapmap]
rs1995057	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1995058	0.95[JPT][hapmap]
rs2006767	0.91[JPT][hapmap]
rs2055077	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs20571	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072696	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2173044	0.90[ASN][1000 genomes]
rs2279701	0.86[JPT][hapmap]
rs2291787	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2307075	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2403104	0.95[JPT][hapmap]
rs2403105	0.85[ASN][1000 genomes]
rs2548281	0.81[CEU][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2645049	0.95[JPT][hapmap]
rs2645053	0.81[ASN][1000 genomes]
rs3087782	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs3758076	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3758077	0.85[ASN][1000 genomes]
rs3758078	0.84[JPT][hapmap]
rs3808539	0.95[JPT][hapmap]
rs4566	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4609189	0.82[JPT][hapmap]
rs4739700	0.91[JPT][hapmap]
rs4740044	0.91[JPT][hapmap]
rs4740045	0.82[JPT][hapmap]
rs4740049	0.95[JPT][hapmap]
rs6605610	0.82[JPT][hapmap]
rs6605611	0.81[JPT][hapmap]
rs66498753	0.81[ASN][1000 genomes]
rs6988475	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6993387	0.91[JPT][hapmap]
rs6994113	0.82[JPT][hapmap]
rs6997458	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7000950	0.91[ASN][1000 genomes]
rs7001359	0.86[JPT][hapmap]
rs7008772	0.91[JPT][hapmap]
rs7011926	0.95[JPT][hapmap]
rs7016369	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs713488	0.84[ASN][1000 genomes]
rs713489	0.84[ASN][1000 genomes]
rs725605	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7818163	0.91[JPT][hapmap]
rs7824715	0.92[ASN][1000 genomes]
rs903895	0.95[JPT][hapmap]
rs903896	0.95[JPT][hapmap]
rs903897	0.95[JPT][hapmap]
rs9286249	0.82[ASN][1000 genomes]
rs931505	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs955007	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9969643	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1022463	chr8:86257031-86547831	Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1804888	chr8:86263098-86986703	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv831377	chr8:86263107-86444141	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028148	chr8:86310570-86553130	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	esv2761206	chr8:86310582-86468868	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9987281	RALYL	cis	parietal	SCAN
rs9987281	C8orf59	cis	cerebellum	SCAN
rs9987281	CA2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86344200-86349600	Weak transcription	NHEK	skin
2	chr8:86344200-86350200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:86344400-86350200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr8:86347400-86349800	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr8:86348200-86349600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:86348200-86349600	Weak transcription	Fetal Muscle Leg	muscle
7	chr8:86348400-86349600	Weak transcription	Psoas Muscle	Psoas
8	chr8:86348600-86349400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:86348800-86350200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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