Variant report

Variant	rs17442853
Chromosome Location	chr12:40544890-40544891
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	12:40543943-40545640..12:40703633-40711447	GM12878	blood:
2	chr12:40543659..40545848-chr12:40705219..40707677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10506145	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10878226	0.85[YRI][hapmap]
rs10878244	0.82[YRI][hapmap]
rs10878246	1.00[YRI][hapmap]
rs11175620	0.85[YRI][hapmap]
rs11175645	0.85[YRI][hapmap]
rs11175655	1.00[YRI][hapmap]
rs11175658	0.85[YRI][hapmap]
rs11175666	0.85[YRI][hapmap]
rs11564122	1.00[YRI][hapmap]
rs11564137	0.86[ASN][1000 genomes]
rs11564194	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564276	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810368	1.00[JPT][hapmap]
rs12827948	1.00[JPT][hapmap]
rs1482282	1.00[JPT][hapmap]
rs1491926	0.86[ASN][1000 genomes]
rs17442108	1.00[JPT][hapmap]
rs17442742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442749	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442756	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442763	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17442805	0.86[ASN][1000 genomes]
rs17443112	0.86[ASN][1000 genomes]
rs17458396	1.00[JPT][hapmap]
rs17458752	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458759	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458766	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458836	1.00[YRI][hapmap]
rs17458974	1.00[YRI][hapmap]
rs17461082	1.00[JPT][hapmap]
rs17461492	0.86[ASN][1000 genomes]
rs17465400	0.86[ASN][1000 genomes]
rs17465519	0.86[ASN][1000 genomes]
rs17465540	0.86[ASN][1000 genomes]
rs17483628	1.00[JPT][hapmap]
rs17491515	1.00[JPT][hapmap]
rs17518057	1.00[JPT][hapmap]
rs17519573	0.85[YRI][hapmap]
rs1873610	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404574	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2638222	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2708404	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28370607	1.00[JPT][hapmap]
rs28370805	1.00[JPT][hapmap]
rs55993200	0.86[ASN][1000 genomes]
rs67985538	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7135678	0.85[YRI][hapmap]
rs726330	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294619	0.85[YRI][hapmap]
rs7294643	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7305155	1.00[YRI][hapmap]
rs7305766	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7306099	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306718	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308399	0.89[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484475	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7969495	1.00[JPT][hapmap]
rs7974522	0.86[ASN][1000 genomes]
rs7974972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17442853	RP11-476D10.1	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40541400-40546600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:40541800-40546600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:40543800-40547200	Weak transcription	HMEC	breast
4	chr12:40544000-40547400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:40544200-40546600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:40544200-40546600	Weak transcription	A549	lung
7	chr12:40544200-40547000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:40544200-40547200	Weak transcription	NHEK	skin

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