Variant report

Variant	rs724742
Chromosome Location	chr12:66666459-66666460
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66665436..66668089-chr12:66696028..66698258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127311	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10748037	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784519	0.92[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10784520	0.96[EUR][1000 genomes]
rs10878396	0.92[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10878397	0.96[EUR][1000 genomes]
rs11176115	0.90[EUR][1000 genomes]
rs11176117	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176120	0.97[EUR][1000 genomes]
rs1168324	0.97[EUR][1000 genomes]
rs12146776	0.86[EUR][1000 genomes]
rs12371662	0.96[EUR][1000 genomes]
rs12423377	0.92[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs12818303	0.87[EUR][1000 genomes]
rs12822967	0.97[EUR][1000 genomes]
rs1603244	0.86[EUR][1000 genomes]
rs1816562	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2047236	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2047237	0.88[EUR][1000 genomes]
rs2088169	0.87[EUR][1000 genomes]
rs2118137	0.87[EUR][1000 genomes]
rs289065	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6421217	0.82[CEU][hapmap]
rs6581669	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137378	0.98[EUR][1000 genomes]
rs7138034	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs724739	0.95[EUR][1000 genomes]
rs7308068	0.82[CEU][hapmap]
rs7315361	0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959802	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972934	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs9971666	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][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	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
4	nsv976747	chr12:66663300-66669568	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs724742	HELB	cis	cerebellum	SCAN
rs724742	HELB	cis	parietal	SCAN
rs724742	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66661200-66666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:66663600-66666600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:66663600-66666800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:66663600-66667400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:66663800-66666800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:66663800-66667000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:66663800-66667400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:66664000-66666600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:66664000-66666800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:66664400-66673000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:66664600-66669800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:66664600-66672800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:66664600-66672800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:66664600-66673000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:66664800-66669600	Weak transcription	Primary T cells from cord blood	blood
16	chr12:66665800-66668800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:66665800-66668800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:66665800-66668800	Weak transcription	Monocytes-CD14+_RO01746	blood

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