Variant report

Variant	rs10784524
Chromosome Location	chr12:66704816-66704817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66694619..66697755-chr12:66702381..66705379,4	MCF-7	breast:
2	chr12:66696693..66698195-chr12:66702307..66704926,2	K562	blood:
3	chr12:66697262..66699095-chr12:66703905..66706309,2	MCF-7	breast:
4	chr12:66703238..66705095-chr12:66713494..66715209,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127311	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10748038	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10748039	0.89[EUR][1000 genomes]
rs10784521	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11176137	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11176138	0.87[CEU][hapmap];0.98[EUR][1000 genomes]
rs11176139	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11176142	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs11176144	0.90[EUR][1000 genomes]
rs12367438	0.91[EUR][1000 genomes]
rs12816200	0.91[EUR][1000 genomes]
rs1495495	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1898305	1.00[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1971302	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3741603	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741605	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs4382951	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4554930	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6581676	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132724	1.00[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7133479	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7298868	0.82[AMR][1000 genomes]
rs7308068	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs7315366	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7316880	1.00[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7956960	0.97[EUR][1000 genomes]
rs7957877	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7959466	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964860	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7969887	0.94[CEU][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7973358	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7978354	1.00[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10784524	HELB	cis	parietal	SCAN
rs10784524	HELB	cis	cerebellum	SCAN
rs10784524	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66696800-66714800	Weak transcription	NHDF-Ad	bronchial
2	chr12:66696800-66716600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:66696800-66717600	Weak transcription	Fetal Brain Male	brain
4	chr12:66696800-66719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:66696800-66723600	Weak transcription	HSMM	muscle
6	chr12:66696800-66734200	Weak transcription	HSMMtube	muscle
7	chr12:66697000-66725000	Weak transcription	Ovary	ovary
8	chr12:66697200-66707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:66697200-66716000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:66697200-66725600	Weak transcription	Fetal Heart	heart
11	chr12:66697200-66733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:66697200-66734800	Weak transcription	Esophagus	oesophagus
13	chr12:66697200-66735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:66697400-66707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:66697400-66714800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:66697400-66719800	Weak transcription	Psoas Muscle	Psoas
18	chr12:66697400-66724800	Weak transcription	Pancreas	Pancrea
19	chr12:66697400-66732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:66697400-66732400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:66697400-66735000	Weak transcription	Right Ventricle	heart
22	chr12:66697600-66714600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:66697800-66725000	Weak transcription	Colonic Mucosa	Colon
24	chr12:66698200-66705800	Weak transcription	Stomach Mucosa	stomach
25	chr12:66698200-66707400	Weak transcription	Small Intestine	intestine
26	chr12:66698200-66707600	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:66698200-66725200	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:66698200-66735000	Weak transcription	Fetal Brain Female	brain
29	chr12:66698400-66706800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:66698400-66713000	Weak transcription	Brain Substantia Nigra	brain
31	chr12:66698400-66714800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:66698400-66732400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:66698400-66734800	Weak transcription	HepG2	liver
34	chr12:66698600-66714800	Weak transcription	Thymus	Thymus
35	chr12:66698800-66706000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:66699000-66706400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:66699000-66708600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:66699000-66735000	Weak transcription	K562	blood
39	chr12:66699400-66705000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr12:66699400-66709800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr12:66700000-66705600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:66700000-66705800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:66700000-66706000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:66700000-66706000	Strong transcription	Fetal Thymus	thymus
45	chr12:66700000-66706400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:66700200-66705400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:66700200-66705800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:66700200-66705800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr12:66700200-66706000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:66700400-66706600	Strong transcription	Primary hematopoietic stem cells	blood

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