Variant report

Variant	rs2088169
Chromosome Location	chr12:66660003-66660004
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	chr12:66653817..66655399-chr12:66657842..66660021,2	K562	blood:
2	chr12:66630936..66633902-chr12:66659450..66661636,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10748037	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs10784519	0.81[CEU][hapmap];0.84[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs10784520	0.86[EUR][1000 genomes]
rs10878396	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs10878397	0.86[EUR][1000 genomes]
rs11176107	0.95[YRI][hapmap]
rs11176115	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176117	0.95[EUR][1000 genomes]
rs11176120	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168324	0.84[EUR][1000 genomes]
rs12371662	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12423377	0.81[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs12818303	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822967	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1603244	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1816562	0.81[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2047236	0.97[EUR][1000 genomes]
rs2047237	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118137	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289065	0.87[EUR][1000 genomes]
rs6581669	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs7137005	0.87[EUR][1000 genomes]
rs7137378	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7138034	0.98[EUR][1000 genomes]
rs724739	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs724742	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs7315361	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs7959802	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7972934	0.93[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9971666	0.93[EUR][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2088169	HELB	cis	parietal	SCAN
rs2088169	HELB	cis	cerebellum	SCAN
rs2088169	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66646000-66662000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:66650800-66663400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:66657600-66660400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:66658200-66663600	Weak transcription	Thymus	Thymus

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