Variant report

Variant	rs9855755
Chromosome Location	chr3:112008750-112008751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111998157..111999865-chr3:112007204..112009141,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10511310	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs10804498	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934163	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934164	1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934165	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709101	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	1.00[ASN][1000 genomes]
rs11923402	1.00[ASN][1000 genomes]
rs11926389	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12489470	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12489616	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12497979	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636943	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs13063452	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs13064242	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs13084103	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084897	0.83[EUR][1000 genomes]
rs13092220	0.81[EUR][1000 genomes]
rs1317295	1.00[ASN][1000 genomes]
rs1317658	1.00[ASN][1000 genomes]
rs13316383	1.00[ASN][1000 genomes]
rs1388858	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs1388859	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1492479	1.00[ASN][1000 genomes]
rs1492489	1.00[CHB][hapmap]
rs17446282	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs17505536	0.83[CEU][hapmap]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2633546	1.00[ASN][1000 genomes]
rs2683891	1.00[ASN][1000 genomes]
rs2683892	1.00[ASN][1000 genomes]
rs28615303	1.00[ASN][1000 genomes]
rs4234409	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4234411	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4321508	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4347976	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4434123	1.00[CHB][hapmap]
rs4507229	1.00[ASN][1000 genomes]
rs4538347	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4622877	1.00[ASN][1000 genomes]
rs4638935	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4682373	0.81[CEU][hapmap]
rs4682393	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682400	1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	1.00[ASN][1000 genomes]
rs56008438	1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56364691	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60949597	1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	1.00[ASN][1000 genomes]
rs62264125	1.00[ASN][1000 genomes]
rs62264128	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	1.00[ASN][1000 genomes]
rs62278768	1.00[ASN][1000 genomes]
rs62278769	1.00[ASN][1000 genomes]
rs62278770	1.00[ASN][1000 genomes]
rs62278771	1.00[ASN][1000 genomes]
rs62278843	1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6764824	0.84[EUR][1000 genomes]
rs6774756	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6781844	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6787323	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6789875	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6795820	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6797177	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6801795	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6804836	1.00[CHB][hapmap]
rs6805112	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6805397	1.00[CHB][hapmap]
rs6805505	0.86[CEU][hapmap]
rs6805887	0.81[CEU][hapmap]
rs73223638	1.00[ASN][1000 genomes]
rs732686	1.00[ASN][1000 genomes]
rs7431999	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7609904	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7612748	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7615460	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7621431	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625249	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs7631673	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636107	1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637676	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7637682	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9288939	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs9288942	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs9810170	1.00[CHB][hapmap]
rs9810421	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9816969	1.00[ASN][1000 genomes]
rs9818407	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	1.00[ASN][1000 genomes]
rs9851141	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9851760	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853669	1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]
rs9871492	0.81[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv877340	chr3:111936961-112013546	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9855755	CD200	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112006600-112012400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:112007400-112010000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:112008200-112008800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:112008600-112012200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:112008600-112012400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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