Variant report

Variant	rs2420387
Chromosome Location	chr11:34512751-34512752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:34508412..34512527-chr11:34512601..34514689,3	MCF-7	breast:
2	chr11:34508032..34510036-chr11:34510118..34513690,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10768074	0.85[EUR][1000 genomes]
rs10836226	0.85[EUR][1000 genomes]
rs10836227	0.85[EUR][1000 genomes]
rs10836228	0.85[EUR][1000 genomes]
rs10836231	0.85[EUR][1000 genomes]
rs10836232	0.87[EUR][1000 genomes]
rs10836233	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs10836235	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10836250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs11032685	0.84[EUR][1000 genomes]
rs11032686	0.85[EUR][1000 genomes]
rs11032687	0.85[EUR][1000 genomes]
rs11032688	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11032689	0.85[EUR][1000 genomes]
rs11032690	0.85[EUR][1000 genomes]
rs11032691	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11032692	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11032693	0.85[EUR][1000 genomes]
rs11032694	0.85[EUR][1000 genomes]
rs11032697	0.81[EUR][1000 genomes]
rs11032701	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11032716	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11032717	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11608027	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12221624	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12285367	0.85[EUR][1000 genomes]
rs12292102	0.83[EUR][1000 genomes]
rs12802066	0.85[EUR][1000 genomes]
rs12803540	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1408034	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1408036	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1408037	0.85[EUR][1000 genomes]
rs1408038	0.85[EUR][1000 genomes]
rs1408039	0.85[EUR][1000 genomes]
rs1408040	0.85[EUR][1000 genomes]
rs16930094	0.87[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17881488	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17884666	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17885743	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1980719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2073059	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[MKK][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2223676	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs2274044	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2284364	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3758730	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60077297	0.83[EUR][1000 genomes]
rs61447308	0.82[EUR][1000 genomes]
rs6484720	0.85[CEU][hapmap];0.84[CHB][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs6484721	0.85[EUR][1000 genomes]
rs6484722	0.90[YRI][hapmap]
rs7106007	0.87[CEU][hapmap];0.84[MEX][hapmap]
rs7111687	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7111765	0.85[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7111903	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs7115206	0.84[EUR][1000 genomes]
rs7117540	0.85[EUR][1000 genomes]
rs7127109	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs7127314	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs7127560	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs7131159	0.84[EUR][1000 genomes]
rs7928156	0.82[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs7929333	0.84[EUR][1000 genomes]
rs7929460	0.80[EUR][1000 genomes]
rs7929574	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7929899	0.85[EUR][1000 genomes]
rs7929931	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7929952	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7930070	0.85[EUR][1000 genomes]
rs7944397	0.84[CHB][hapmap]
rs7947841	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][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	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2420387	CAT	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34511600-34512800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:34512000-34512800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:34512200-34517200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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