Variant report

Variant	rs10958230
Chromosome Location	chr8:85838265-85838266
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10046686	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10081441	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10088722	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10091232	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10091245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10094238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10094828	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10095636	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10095682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10099017	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10100687	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10100806	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10104630	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10104687	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10105658	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10109018	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110570	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10110879	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1025232	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958229	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10958232	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10958233	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11775584	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12542468	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12604	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675186	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13267859	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13273360	0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1365668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1365677	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1365678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404365	0.94[ASN][1000 genomes]
rs1524642	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17811680	0.85[ASN][1000 genomes]
rs1851973	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1946400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991347	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991348	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991349	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991352	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2059678	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2059680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081673	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2140688	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28592585	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34327710	0.84[ASN][1000 genomes]
rs35068782	0.86[ASN][1000 genomes]
rs35382421	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3900098	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3937521	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3942601	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4740035	0.85[ASN][1000 genomes]
rs6990756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7003643	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7008839	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7010343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7832097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838564	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7838940	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9298433	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9650296	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs965734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9692810	0.94[ASN][1000 genomes]
rs9692962	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs9693371	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs987477	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv891120	chr8:85749529-85890857	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10958230	C8orf59	cis	cerebellum	SCAN
rs10958230	LRRCC1	cis	cerebellum	SCAN
rs10958230	LRRCC1	cis	Esophagus Mucosa	GTEx
rs10958230	C8orf59	cis	parietal	SCAN
rs10958230	LRRCC1	cis	Artery Tibial	GTEx
rs10958230	CA13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:85822600-85841400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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