Variant report

Variant	rs10784523
Chromosome Location	chr12:66697400-66697401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66697243..66701678-chr12:66713455..66715923,3	K562	blood:
2	chr12:66697262..66699095-chr12:66703905..66706309,2	MCF-7	breast:
3	chr12:66523311..66525203-chr12:66696051..66697589,2	MCF-7	breast:
4	chr12:66684746..66687398-chr12:66696946..66699737,2	MCF-7	breast:
5	chr12:66563056..66564656-chr12:66694946..66697705,2	MCF-7	breast:
6	chr12:66696693..66698195-chr12:66702307..66704926,2	K562	blood:
7	chr12:66696640..66699330-chr12:66723248..66725876,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127311	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000222744	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1009211	0.95[EUR][1000 genomes]
rs10878401	0.95[EUR][1000 genomes]
rs10878402	0.94[EUR][1000 genomes]
rs10878403	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176125	0.95[EUR][1000 genomes]
rs11176126	0.95[EUR][1000 genomes]
rs11176132	0.94[EUR][1000 genomes]
rs11176138	0.84[AFR][1000 genomes]
rs11610967	0.86[EUR][1000 genomes]
rs12146707	0.98[EUR][1000 genomes]
rs12146757	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12146776	0.83[EUR][1000 genomes]
rs12822052	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1370125	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1921013	0.96[EUR][1000 genomes]
rs1971302	0.87[AFR][1000 genomes]
rs2028095	0.92[EUR][1000 genomes]
rs2118138	0.99[EUR][1000 genomes]
rs2118139	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118140	0.99[EUR][1000 genomes]
rs2904497	0.93[EUR][1000 genomes]
rs3741604	0.98[EUR][1000 genomes]
rs3741605	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4430553	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6421217	0.88[EUR][1000 genomes]
rs6581672	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131920	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7306114	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308068	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7964860	0.87[AFR][1000 genomes]
rs7968129	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs974349	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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
rs10784523	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs10784523	HELB	cis	Muscle Skeletal	GTEx
rs10784523	HELB	cis	Nerve Tibial	GTEx

Chromatin state (count:141 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66694800-66698400	Active TSS	Rectal Smooth Muscle	rectum
2	chr12:66695200-66698000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:66695400-66698400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr12:66695600-66697400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:66695600-66697400	Active TSS	HMEC	breast
6	chr12:66695600-66697600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr12:66695600-66697600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr12:66695600-66697600	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr12:66695600-66697800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:66695600-66697800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr12:66695600-66697800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:66695600-66697800	Active TSS	Colonic Mucosa	Colon
13	chr12:66695800-66697400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:66695800-66697600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:66695800-66697600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:66695800-66697800	Active TSS	Small Intestine	intestine
17	chr12:66695800-66698400	Active TSS	Fetal Kidney	kidney
18	chr12:66695800-66698600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:66695800-66698600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr12:66695800-66698600	Active TSS	Duodenum Mucosa	Duodenum
21	chr12:66695800-66698800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:66695800-66700000	Active TSS	GM12878-XiMat	blood
23	chr12:66696000-66697600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:66696000-66697800	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr12:66696000-66697800	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr12:66696000-66698000	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr12:66696000-66698000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr12:66696000-66698000	Active TSS	Primary T cells from cord blood	blood
29	chr12:66696000-66698000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr12:66696000-66698000	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr12:66696000-66698200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:66696000-66698800	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr12:66696400-66697400	Flanking Active TSS	Fetal Thymus	thymus
34	chr12:66696400-66697800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr12:66696400-66698400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr12:66696400-66698400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr12:66696400-66698400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:66696600-66698800	Flanking Active TSS	Dnd41	blood
39	chr12:66696800-66697400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr12:66696800-66697400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:66696800-66697400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:66696800-66698800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr12:66696800-66701800	Weak transcription	Left Ventricle	heart
44	chr12:66696800-66702000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:66696800-66702000	Weak transcription	Aorta	Aorta
46	chr12:66696800-66703800	Weak transcription	Lung	lung
47	chr12:66696800-66714800	Weak transcription	NHDF-Ad	bronchial
48	chr12:66696800-66716600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:66696800-66717600	Weak transcription	Fetal Brain Male	brain
50	chr12:66696800-66719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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