Variant report

Variant	rs1168324
Chromosome Location	chr12:66672907-66672908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:66672889-66673290	A549	lung:	n/a	chr12:66673101-66673120
2	CTCF	chr12:66672873-66673269	K562	blood:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
3	CTCF	chr12:66672905-66673190	H1-hESC	embryonic stem cell:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
4	RAD21	chr12:66672837-66673334	MCF-7	breast:	n/a	chr12:66673101-66673120
5	CTCF	chr12:66672878-66673366	MCF-7	breast:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
6	RAD21	chr12:66672443-66673495	SK-N-SH	brain:	n/a	chr12:66673101-66673120
7	CTCF	chr12:66672851-66673373	HCT-116	colon:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
8	CTCF	chr12:66672886-66673258	H1-hESC	embryonic stem cell:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
9	USF2	chr12:66672900-66672999	HepG2	liver:	n/a	n/a
10	RAD21	chr12:66672844-66673306	SK-N-SH_RA	brain:	n/a	chr12:66673101-66673120
11	RAD21	chr12:66672817-66673398	MCF-7	breast:	n/a	chr12:66673101-66673120
12	CTCF	chr12:66672763-66673493	HCT-116	colon:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
13	RAD21	chr12:66672894-66673219	SK-N-SH_RA	brain:	n/a	chr12:66673101-66673120
14	RAD21	chr12:66672871-66673491	HCT-116	colon:	n/a	chr12:66673101-66673120
15	RAD21	chr12:66672875-66673307	ECC-1	luminal epithelium:	n/a	chr12:66673101-66673120
16	CTCF	chr12:66672714-66673429	A549	lung:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
17	SMC3	chr12:66672854-66673401	SK-N-SH	brain:	n/a	chr12:66673102-66673116
18	CTCF	chr12:66672800-66673451	SK-N-SH	brain:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
19	RAD21	chr12:66672855-66673384	ECC-1	luminal epithelium:	n/a	chr12:66673101-66673120
20	CTCF	chr12:66672853-66673260	MCF-7	breast:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
21	CTCF	chr12:66672902-66673305	IMR90	lung:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
22	RAD21	chr12:66672854-66673449	HCT-116	colon:	n/a	chr12:66673101-66673120
23	CTCF	chr12:66672864-66673239	HepG2	liver:	n/a	chr12:66673102-66673123 chr12:66673100-66673118

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66672595..66673805-chr12:66802877..66803711,5	MCF-7	breast:
2	chr12:66561793..66564374-chr12:66672435..66674661,2	MCF-7	breast:

Variant related genes	Relation type
PDCL3P7	TF binding region
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10748037	0.97[EUR][1000 genomes]
rs10784519	0.98[EUR][1000 genomes]
rs10784520	0.98[EUR][1000 genomes]
rs10878396	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10878397	0.98[EUR][1000 genomes]
rs11176115	0.87[EUR][1000 genomes]
rs11176117	0.88[EUR][1000 genomes]
rs11176120	0.94[EUR][1000 genomes]
rs12146776	0.88[EUR][1000 genomes]
rs12371662	0.93[EUR][1000 genomes]
rs12423377	0.98[EUR][1000 genomes]
rs12818303	0.84[EUR][1000 genomes]
rs12822967	0.94[EUR][1000 genomes]
rs1603244	0.83[EUR][1000 genomes]
rs1816562	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2043668	0.81[ASN][1000 genomes]
rs2047236	0.85[EUR][1000 genomes]
rs2047237	0.85[EUR][1000 genomes]
rs2088169	0.84[EUR][1000 genomes]
rs2118137	0.85[EUR][1000 genomes]
rs289065	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581669	0.96[EUR][1000 genomes]
rs7137005	0.97[EUR][1000 genomes]
rs7137378	0.95[EUR][1000 genomes]
rs7138034	0.86[EUR][1000 genomes]
rs724739	0.92[EUR][1000 genomes]
rs724742	0.97[EUR][1000 genomes]
rs7315361	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7959802	0.97[EUR][1000 genomes]
rs7972934	0.95[EUR][1000 genomes]
rs9971666	0.89[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1168324	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs1168324	HELB	cis	Muscle Skeletal	GTEx
rs1168324	HELB	cis	brain	BrainEAC
rs1168324	HELB	cis	Nerve Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66664400-66673000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:66664600-66673000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:66669600-66673000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:66670200-66673000	Weak transcription	Primary T cells from cord blood	blood
5	chr12:66672400-66673000	Enhancers	HUVEC	blood vessel
6	chr12:66672600-66674800	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr12:66672600-66675000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr12:66672800-66675000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:66672800-66675200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:66672800-66675200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:66672800-66675200	Enhancers	Primary T helper cells PMA-I stimulated	--

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