Variant report

Variant	rs1952122
Chromosome Location	chr10:90279372-90279373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10736357	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10736358	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788604	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs10788605	0.84[AFR][1000 genomes]
rs10788606	0.83[ASW][hapmap]
rs10887827	0.84[AFR][1000 genomes]
rs10887829	0.83[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs11202772	0.88[JPT][hapmap]
rs1183901	0.86[CHB][hapmap]
rs12219242	0.81[JPT][hapmap]
rs1325903	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325907	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[LWK][hapmap]
rs1359580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409134	0.88[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1925937	1.00[ASN][1000 genomes]
rs1980812	1.00[ASN][1000 genomes]
rs2153856	0.84[LWK][hapmap];0.85[YRI][hapmap]
rs2437871	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs2437872	0.85[CHB][hapmap]
rs2437878	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[LWK][hapmap]
rs2477952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2477957	0.85[CHB][hapmap]
rs2488271	0.86[CHB][hapmap]
rs2576166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2576174	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[LWK][hapmap]
rs2576179	0.86[CHB][hapmap]
rs2576180	0.84[CHB][hapmap]
rs2765444	0.86[CHB][hapmap]
rs7075544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7096710	0.80[LWK][hapmap];0.85[MEX][hapmap]
rs725683	0.86[CHB][hapmap]
rs725684	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs745354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7917100	0.81[CHB][hapmap];0.96[YRI][hapmap]

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	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1952122	BTAF1	cis	cerebellum	SCAN
rs1952122	LIPM	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90269000-90279600	Weak transcription	Left Ventricle	heart
2	chr10:90274800-90279600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:90275400-90281200	Weak transcription	Ovary	ovary
4	chr10:90278800-90279800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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