Variant report

Variant	rs12566700
Chromosome Location	chr1:171747180-171747181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171715474..171717063-chr1:171747141..171749342,2	K562	blood:
2	chr1:171746858..171748372-chr1:171748853..171751746,3	K562	blood:
3	chr1:171734034..171736178-chr1:171746102..171748315,3	K562	blood:
4	chr1:171715364..171718014-chr1:171745246..171747698,2	MCF-7	breast:
5	chr1:171709792..171712103-chr1:171746642..171748516,2	K562	blood:
6	chr1:171738704..171740744-chr1:171745299..171748129,2	MCF-7	breast:
7	chr1:171738793..171742009-chr1:171745293..171748243,3	K562	blood:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10798634	0.87[CHB][hapmap]
rs10798636	0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs10798667	0.86[ASN][1000 genomes]
rs10913644	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11579330	0.84[ASW][hapmap]
rs11587288	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs12032340	0.86[CHB][hapmap];0.88[MEX][hapmap]
rs12034454	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs16843385	0.88[ASN][1000 genomes]
rs2232812	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs2232816	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs2232818	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.93[ASN][1000 genomes]
rs2232826	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.91[ASN][1000 genomes]
rs2294717	0.87[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs3753538	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs56178029	0.91[ASN][1000 genomes]
rs57476157	0.84[ASN][1000 genomes]
rs59302445	0.90[ASN][1000 genomes]
rs60502293	0.87[ASN][1000 genomes]
rs60956160	0.85[ASN][1000 genomes]
rs6425405	0.87[CHB][hapmap]
rs6425423	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6425438	0.81[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs6425439	0.85[ASN][1000 genomes]
rs6684594	0.91[ASN][1000 genomes]
rs6691222	0.90[JPT][hapmap]
rs6695502	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs72703115	0.86[ASN][1000 genomes]
rs7541192	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7542116	0.87[CHB][hapmap]
rs7543608	0.95[ASN][1000 genomes]
rs7548462	0.91[ASN][1000 genomes]
rs7554793	0.81[CEU][hapmap]
rs7860	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs909958	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs941942	0.87[CHB][hapmap];0.84[ASN][1000 genomes]

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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12566700	SELL	cis	cerebellum	SCAN
rs12566700	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs12566700	SNORD79	cis	parietal	SCAN
rs12566700	DNM3	cis	cerebellum	SCAN
rs12566700	METTL13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171740000-171749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:171745400-171749400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:171746400-171747200	Enhancers	K562	blood
4	chr1:171746600-171747200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:171747000-171749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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