Variant report

Variant	rs12488831
Chromosome Location	chr3:50980398-50980399
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50979915..50982588-chr3:50988969..50990913,2	K562	blood:
2	chr3:50978925..50980444-chr8:43095229..43096751,2	K562	blood:
3	chr3:50979924..50980442-chr8:43092410..43092931,4	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12485524	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12486828	0.91[ASN][1000 genomes]
rs12487821	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs12488700	0.93[JPT][hapmap];0.83[YRI][hapmap]
rs12488948	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490502	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12490519	0.91[ASN][1000 genomes]
rs12491206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12491402	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12492367	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12492850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494214	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12494708	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12494776	0.91[ASN][1000 genomes]
rs12495399	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12496601	0.89[ASN][1000 genomes]
rs12496621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12497067	0.90[ASN][1000 genomes]
rs17051468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2125368	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2262847	0.94[ASN][1000 genomes]
rs2355707	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4073739	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4078296	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4323036	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4688695	0.89[ASN][1000 genomes]
rs4688696	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs4688697	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4688752	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4927961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs4927975	0.92[YRI][hapmap]
rs56844171	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58356214	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58720544	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60184902	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60552386	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60602904	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs60882641	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60917457	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61557316	0.82[ASN][1000 genomes]
rs61627377	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61676409	0.88[ASN][1000 genomes]
rs6446239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72937251	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72937253	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72937262	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72937265	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72937299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72939228	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72942530	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72942567	0.91[ASN][1000 genomes]
rs7372342	0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7427526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7427615	0.94[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1004881	chr3:50900793-51032918	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv536568	chr3:50900793-51032918	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1803890	chr3:50966037-50987194	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3384945	chr3:50980217-50980476	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3409618	chr3:50980386-50980701	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12488831	HEMK1	cis	multi-tissue	Pritchard
rs12488831	HEMK	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50973200-50983400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:50974000-50991200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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