Variant report

Variant	rs1921013
Chromosome Location	chr12:66695500-66695501
allele	G/T
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	MXI1	chr12:66695107-66697212	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr12:66695444-66695584	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr12:66695369-66695513	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:66695366-66695513	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66563056..66564656-chr12:66694946..66697705,2	MCF-7	breast:
2	chr12:66687583..66689264-chr12:66693938..66695538,2	MCF-7	breast:

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

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1009211	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784523	0.96[EUR][1000 genomes]
rs10878401	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878402	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878403	0.92[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs11176125	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176126	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176132	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176137	0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs11176142	0.83[CHB][hapmap]
rs11610967	0.86[CEU][hapmap];0.88[CHB][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12146707	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12146757	0.98[EUR][1000 genomes]
rs12146776	0.82[EUR][1000 genomes]
rs12822052	0.95[EUR][1000 genomes]
rs1370125	0.93[EUR][1000 genomes]
rs2028095	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118138	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2118139	0.96[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs2118140	0.96[CEU][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2904497	0.94[EUR][1000 genomes]
rs3741604	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741605	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4430553	0.96[CEU][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6421217	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581672	0.94[EUR][1000 genomes]
rs7131920	0.97[EUR][1000 genomes]
rs7306114	0.93[EUR][1000 genomes]
rs7308068	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs7968129	0.93[EUR][1000 genomes]
rs974349	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1921013	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs1921013	HELB	cis	Muscle Skeletal	GTEx
rs1921013	HELB	cis	cerebellum	SCAN
rs1921013	C12orf56	cis	cerebellum	SCAN
rs1921013	HELB	cis	Nerve Tibial	GTEx
rs1921013	HELB	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66688000-66695600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr12:66691200-66695600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:66691400-66695600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:66691400-66695600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:66691400-66695600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:66691600-66695600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:66691600-66695600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:66691600-66695600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:66694000-66695600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:66694800-66695600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:66694800-66695600	Enhancers	Brain Cingulate Gyrus	brain
12	chr12:66694800-66695600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr12:66694800-66695600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr12:66694800-66698400	Active TSS	Rectal Smooth Muscle	rectum
15	chr12:66695000-66695600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:66695000-66695600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:66695000-66695600	Active TSS	Brain Anterior Caudate	brain
18	chr12:66695200-66695600	Enhancers	Primary T cells from cord blood	blood
19	chr12:66695200-66695600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:66695200-66695600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:66695200-66695600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:66695200-66695600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr12:66695200-66695600	Bivalent Enhancer	Thymus	Thymus
24	chr12:66695200-66697200	Active TSS	Stomach Smooth Muscle	stomach
25	chr12:66695200-66698000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr12:66695400-66695600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:66695400-66695600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:66695400-66695600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:66695400-66695600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr12:66695400-66695600	Active TSS	Primary hematopoietic stem cells	blood
31	chr12:66695400-66695600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr12:66695400-66695600	Enhancers	Duodenum Mucosa	Duodenum
33	chr12:66695400-66695600	Active TSS	Fetal Brain Female	brain
34	chr12:66695400-66695600	Enhancers	Fetal Thymus	thymus
35	chr12:66695400-66695600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:66695400-66695600	Active TSS	Monocytes-CD14+_RO01746	blood
37	chr12:66695400-66695800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr12:66695400-66695800	Active TSS	Brain Germinal Matrix	brain
39	chr12:66695400-66696000	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr12:66695400-66696000	Flanking Active TSS	Dnd41	blood
41	chr12:66695400-66696400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:66695400-66696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:66695400-66696400	Active TSS	Adipose Nuclei	Adipose
44	chr12:66695400-66697000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:66695400-66697000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:66695400-66697000	Active TSS	Brain Hippocampus Middle	brain
47	chr12:66695400-66698400	Active TSS	Rectal Mucosa Donor 29	rectum

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