Variant report

Variant	rs9692962
Chromosome Location	chr8:85896920-85896921
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	EP300	chr8:85896854-85896999	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:85891336..85894175-chr8:85894387..85896944,2	MCF-7	breast:

Variant related genes	Relation type
IGJP1	TF binding region
ENSG00000253655	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10046686	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs10081441	0.94[ASN][1000 genomes]
rs10088120	0.90[JPT][hapmap]
rs10088722	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10091232	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10091245	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10094238	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10094828	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10095636	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10095682	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs10099017	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10100687	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10100806	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10104630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10104687	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10105658	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10109018	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10110570	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10110879	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1025232	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958229	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958230	0.94[ASN][1000 genomes]
rs10958232	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958233	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11261468	0.82[JPT][hapmap]
rs11775584	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12542468	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12604	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12675186	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13267859	0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13269739	0.90[JPT][hapmap]
rs13273360	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1365668	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1365677	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1365678	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404365	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524642	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17811680	0.91[ASN][1000 genomes]
rs1851973	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1946400	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991347	0.97[ASN][1000 genomes]
rs1991348	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991349	0.97[ASN][1000 genomes]
rs1991350	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991351	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991352	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2059678	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059679	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2059680	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081673	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140688	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403088	0.82[JPT][hapmap]
rs2712	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28592585	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2896454	0.90[JPT][hapmap]
rs34103685	0.90[JPT][hapmap]
rs34327710	0.84[ASN][1000 genomes]
rs35068782	0.91[ASN][1000 genomes]
rs35382421	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3779899	0.90[JPT][hapmap]
rs3900098	0.97[ASN][1000 genomes]
rs3937521	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3942601	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4740035	0.91[ASN][1000 genomes]
rs6605624	0.81[JPT][hapmap]
rs6990756	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7003643	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7008839	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7010343	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7015758	0.90[JPT][hapmap]
rs7829050	0.90[JPT][hapmap]
rs7829144	0.82[JPT][hapmap]
rs7832097	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7838564	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7838940	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs7841142	0.82[JPT][hapmap]
rs9298433	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9650296	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965734	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9692810	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9693371	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987477	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][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	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv427823	chr8:85538522-86009068	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv428203	chr8:85834033-86009068	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9692962	C8orf59	cis	parietal	SCAN
rs9692962	C8orf59	cis	cerebellum	SCAN
rs9692962	LRRCC1	cis	Esophagus Mucosa	GTEx
rs9692962	LRRCC1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:85896200-85897200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:85896200-85897200	Enhancers	HMEC	breast
3	chr8:85896600-85897000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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