Variant report

Variant	rs12402371
Chromosome Location	chr1:166147182-166147183
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	chr1:166146882..166148788-chr1:166149453..166151737,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10494453	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10494455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10494456	0.81[ASN][1000 genomes]
rs10753713	0.81[ASN][1000 genomes]
rs10753714	0.81[ASN][1000 genomes]
rs10800198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800199	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10800200	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10800202	0.81[ASN][1000 genomes]
rs10918369	0.90[TSI][hapmap]
rs10918381	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918383	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918384	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918385	0.94[EUR][1000 genomes]
rs10918387	0.81[ASN][1000 genomes]
rs10918388	0.81[ASN][1000 genomes]
rs12023523	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12028067	0.81[ASN][1000 genomes]
rs12031538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12076837	0.92[EUR][1000 genomes]
rs12126834	0.94[EUR][1000 genomes]
rs12136704	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12144426	0.93[EUR][1000 genomes]
rs12409766	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432119	0.94[EUR][1000 genomes]
rs1529642	0.92[EUR][1000 genomes]
rs1530889	0.92[EUR][1000 genomes]
rs1551179	0.96[EUR][1000 genomes]
rs1560570	0.80[ASN][1000 genomes]
rs16856734	0.81[ASN][1000 genomes]
rs1864791	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116519	0.89[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs28568389	0.81[ASN][1000 genomes]
rs4074897	0.90[TSI][hapmap]
rs4147072	0.81[ASN][1000 genomes]
rs4391646	0.80[ASN][1000 genomes]
rs4556335	0.81[ASN][1000 genomes]
rs4656481	0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs4656484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4657530	0.94[EUR][1000 genomes]
rs61835144	0.82[ASN][1000 genomes]
rs61835149	0.81[ASN][1000 genomes]
rs61835150	0.81[ASN][1000 genomes]
rs61835151	0.81[ASN][1000 genomes]
rs6426968	0.90[TSI][hapmap]
rs6658248	0.82[ASN][1000 genomes]
rs6658513	0.82[ASN][1000 genomes]
rs6681924	0.89[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs6696964	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698285	0.82[TSI][hapmap]
rs6698973	0.90[TSI][hapmap]
rs6700193	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs715421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7513325	0.90[TSI][hapmap]
rs7548172	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[EUR][1000 genomes]
rs7552225	0.81[ASN][1000 genomes]
rs9787101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9787239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv3332610	chr1:166111288-166282689	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12402371	PBX1	cis	cerebellum	SCAN
rs12402371	CD48	cis	parietal	SCAN
rs12402371	RCSD1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166143200-166151400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:166143600-166148200	Weak transcription	Gastric	stomach
3	chr1:166143800-166154200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:166146800-166147600	Enhancers	Pancreas	Pancrea
5	chr1:166147000-166147400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:166147000-166147600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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