Variant report

Variant	rs10460866
Chromosome Location	chr3:160372844-160372845
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160367747..160369852-chr3:160370471..160373383,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10936203	0.90[CHB][hapmap]
rs11711627	0.85[ASN][1000 genomes]
rs11712392	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713230	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11720693	0.94[EUR][1000 genomes]
rs12639488	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs13062928	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13065269	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13072556	0.90[EUR][1000 genomes]
rs13074231	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13075424	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13085507	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1403045	0.83[CEU][hapmap]
rs16831337	0.84[CEU][hapmap]
rs17236494	0.82[CHB][hapmap]
rs17826257	0.90[CHB][hapmap]
rs1879797	0.87[CEU][hapmap]
rs1882125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920650	0.85[ASN][1000 genomes]
rs2141668	0.85[ASN][1000 genomes]
rs2178451	0.83[ASN][1000 genomes]
rs2367209	0.84[EUR][1000 genomes]
rs34058107	0.93[EUR][1000 genomes]
rs34444753	0.89[EUR][1000 genomes]
rs35008770	0.85[ASN][1000 genomes]
rs35498840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4133253	0.84[CEU][hapmap]
rs4679903	0.85[ASN][1000 genomes]
rs4679904	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57718211	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60339919	0.89[EUR][1000 genomes]
rs6792943	0.89[EUR][1000 genomes]
rs6806755	0.84[CEU][hapmap]
rs71314011	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610939	0.84[CEU][hapmap]
rs7633839	1.00[CEU][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes]
rs7634255	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv2757019	chr3:160351021-160380161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2759194	chr3:160351021-160380161	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10460866	KLRB1	trans	parietal	SCAN
rs10460866	IFT80	cis	parietal	SCAN
rs10460866	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160372600-160376000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:160372600-160385200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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