Variant report

Variant	rs10958542
Chromosome Location	chr8:39089941-39089942
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:39080941..39082777-chr8:39089064..39090963,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10094307	0.83[YRI][hapmap]
rs10099331	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10104527	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10958540	1.00[ASW][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs11776234	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11996112	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12675132	0.82[JPT][hapmap]
rs4273822	1.00[ASW][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs4515515	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs4733913	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4733986	1.00[ASW][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs4733994	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6474126	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs6986118	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6988280	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs6989252	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6994939	0.89[CEU][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs7009007	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7016661	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7357360	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7830326	1.00[ASW][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015907	chr8:38967169-39718559	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv539550	chr8:38967169-39718559	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1027443	chr8:38993423-39181079	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv539551	chr8:38993423-39181079	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv428198	chr8:39069309-39405724	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1019752	chr8:39087542-39371410	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10958542	SGK196	cis	parietal	SCAN
rs10958542	TM2D2	cis	cerebellum	SCAN
rs10958542	ADAM32	cis	Nerve Tibial	GTEx
rs10958542	TM2D2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39076200-39097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:39083200-39097800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr8:39085200-39090400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:39089800-39090000	Enhancers	HMEC	breast

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