Variant report

Variant	rs10784519
Chromosome Location	chr12:66673432-66673433
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	chr12:66672443-66673495	SK-N-SH	brain:	n/a	chr12:66673101-66673120
2	CTCF	chr12:66672763-66673493	HCT-116	colon:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
3	RAD21	chr12:66672871-66673491	HCT-116	colon:	n/a	chr12:66673101-66673120
4	CTCF	chr12:66672800-66673451	SK-N-SH	brain:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
5	RAD21	chr12:66672854-66673449	HCT-116	colon:	n/a	chr12:66673101-66673120

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: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009211	0.80[EUR][1000 genomes]
rs10748037	1.00[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10784520	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878396	1.00[CEU][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs10878397	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878401	0.80[EUR][1000 genomes]
rs10878402	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs10878403	0.81[CEU][hapmap]
rs11176115	0.89[EUR][1000 genomes]
rs11176117	0.87[EUR][1000 genomes]
rs11176120	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176125	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11176126	0.80[EUR][1000 genomes]
rs11176132	0.80[EUR][1000 genomes]
rs11610967	0.81[CHB][hapmap]
rs1168324	0.98[EUR][1000 genomes]
rs12146776	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371662	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12423377	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818303	0.86[EUR][1000 genomes]
rs12819421	0.85[CHB][hapmap]
rs12822967	0.96[EUR][1000 genomes]
rs1603244	0.85[EUR][1000 genomes]
rs1816562	1.00[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs2047236	0.84[EUR][1000 genomes]
rs2047237	0.87[EUR][1000 genomes]
rs2088169	0.86[EUR][1000 genomes]
rs2118137	0.86[EUR][1000 genomes]
rs289065	0.95[EUR][1000 genomes]
rs2904497	0.81[EUR][1000 genomes]
rs6421217	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs6581669	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7137005	0.96[EUR][1000 genomes]
rs7137378	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7138034	0.85[EUR][1000 genomes]
rs724739	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs724742	0.92[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs7308068	0.83[CEU][hapmap]
rs7315361	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7959802	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7972934	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9971666	0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10784519	HELB	cis	cerebellum	SCAN
rs10784519	HELB	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66672600-66674800	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr12:66672600-66675000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr12:66672800-66675000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:66672800-66675200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr12:66672800-66675200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr12:66672800-66675200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:66673000-66674000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:66673000-66674400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:66673000-66674600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:66673000-66674800	Enhancers	Primary T cells from cord blood	blood
11	chr12:66673000-66674800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:66673000-66674800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr12:66673000-66675000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr12:66673000-66675200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:66673200-66673600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:66673200-66673800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr12:66673200-66674600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:66673400-66674800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:66673400-66674800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:66673400-66674800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:66673400-66674800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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