Variant report

Variant	rs12099979
Chromosome Location	chr12:56454989-56454990
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	chr12:56453956..56456454-chr12:56472074..56474729,2	K562	blood:
2	chr12:56451618..56456572-chr12:56471956..56474542,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065361	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11171713	0.87[AMR][1000 genomes]
rs11171714	0.87[AMR][1000 genomes]
rs12810011	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12815302	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12815387	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs12815488	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12817471	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12817765	0.87[AMR][1000 genomes]
rs12818756	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12831468	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12831884	0.88[CEU][hapmap]
rs1614219	0.98[EUR][1000 genomes]
rs1689511	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs1701706	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs17118206	0.87[AMR][1000 genomes]
rs17118208	0.87[AMR][1000 genomes]
rs17118262	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131569	0.92[EUR][1000 genomes]
rs2229046	0.81[AMR][1000 genomes]
rs2456972	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs2658479	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs34071823	0.87[AMR][1000 genomes]
rs34228181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34273234	0.81[AMR][1000 genomes]
rs34303864	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34406511	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34485293	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34507011	0.91[EUR][1000 genomes]
rs34602183	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34650555	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34921584	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34962186	0.87[AMR][1000 genomes]
rs35485002	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35662491	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35666826	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35961650	0.94[EUR][1000 genomes]
rs36035578	0.81[AMR][1000 genomes]
rs4759022	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs4759239	0.94[EUR][1000 genomes]
rs67594137	0.81[AMR][1000 genomes]
rs71447768	0.87[AMR][1000 genomes]
rs71459326	0.87[AMR][1000 genomes]
rs71459327	0.87[AMR][1000 genomes]
rs71459334	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459336	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71459339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459342	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7298818	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7300772	0.98[EUR][1000 genomes]
rs772919	0.89[EUR][1000 genomes]
rs772922	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs772923	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs773115	0.94[EUR][1000 genomes]
rs7963590	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7977537	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12099979	SUOX	cis	Thyroid	GTEx
rs12099979	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
2	chr12:56440800-56455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:56449200-56456400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:56454400-56456000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:56454400-56456200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:56454400-56456600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:56454400-56456600	Weak transcription	HMEC	breast
8	chr12:56454400-56456800	Weak transcription	NHEK	skin
9	chr12:56454400-56457000	Weak transcription	Osteobl	bone
10	chr12:56454400-56467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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