Variant report

Variant	rs12066979
Chromosome Location	chr1:226271766-226271767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226184976..226187995-chr1:226271007..226274594,3	K562	blood:
2	chr1:226271235..226271796-chrX:15692885..15693487,2	Hela-S3	cervix:
3	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
4	chr1:226248789..226253333-chr1:226269675..226273948,8	MCF-7	breast:
5	chr1:226270770..226272699-chr1:226374583..226377096,2	MCF-7	breast:
6	chr1:226185497..226187877-chr1:226269946..226272750,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000223570	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000186312	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10753411	0.87[LWK][hapmap];0.87[YRI][hapmap]
rs10799335	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915930	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915931	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915932	0.94[EUR][1000 genomes]
rs12060155	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12086044	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12096468	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12096737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377470	0.81[ASN][1000 genomes]
rs28737326	0.80[ASN][1000 genomes]
rs3768543	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4012723	0.81[ASN][1000 genomes]
rs4271181	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs61835246	0.84[ASN][1000 genomes]
rs61835247	0.80[ASN][1000 genomes]
rs6426106	0.82[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6678547	0.88[EUR][1000 genomes]
rs6681021	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692329	0.93[EUR][1000 genomes]
rs6692849	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700189	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7522361	0.83[ASN][1000 genomes]
rs7543135	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12066979	H3F3A	cis	Esophagus Muscularis	GTEx
rs12066979	H3F3A	cis	Nerve Tibial	GTEx
rs12066979	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs12066979	H3F3A	cis	Artery Tibial	GTEx
rs12066979	H3F3A	cis	Esophagus Mucosa	GTEx
rs12066979	H3F3A	cis	Adipose Subcutaneous	GTEx
rs12066979	H3F3A	cis	Muscle Skeletal	GTEx
rs12066979	H3F3A	cis	Artery Aorta	GTEx
rs12066979	H3F3A	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226270400-226271800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:226270400-226271800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr1:226270400-226271800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr1:226270400-226271800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:226270400-226271800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:226270400-226271800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr1:226270400-226271800	Flanking Active TSS	Liver	Liver
8	chr1:226270400-226271800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:226270400-226271800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr1:226270400-226271800	Flanking Active TSS	Dnd41	blood
11	chr1:226270400-226272000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:226270400-226272000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:226270400-226272000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:226270400-226272000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr1:226270400-226272000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr1:226270400-226272000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:226270400-226272000	Flanking Active TSS	Colonic Mucosa	Colon
18	chr1:226270400-226272000	Active TSS	Rectal Smooth Muscle	rectum
19	chr1:226270600-226271800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr1:226270600-226271800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:226270600-226271800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:226270600-226271800	Active TSS	Aorta	Aorta
23	chr1:226270600-226271800	Active TSS	Fetal Kidney	kidney
24	chr1:226270600-226271800	Active TSS	Right Atrium	heart
25	chr1:226270600-226271800	Active TSS	HSMMtube	muscle
26	chr1:226270600-226271800	Active TSS	NHDF-Ad	bronchial
27	chr1:226270600-226272000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:226270600-226272000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:226270600-226272000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:226270600-226272000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr1:226270600-226272000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:226270600-226272000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:226270600-226272000	Active TSS	Brain Angular Gyrus	brain
34	chr1:226270600-226272000	Active TSS	Brain Cingulate Gyrus	brain
35	chr1:226270600-226272000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:226270600-226272000	Enhancers	Fetal Brain Male	brain
37	chr1:226270600-226272000	Active TSS	Psoas Muscle	Psoas
38	chr1:226270600-226272000	Active TSS	Hela-S3	cervix
39	chr1:226270800-226271800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:226270800-226271800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:226270800-226271800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:226270800-226271800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:226270800-226271800	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr1:226270800-226271800	Bivalent/Poised TSS	Fetal Stomach	stomach
45	chr1:226270800-226271800	Active TSS	Left Ventricle	heart
46	chr1:226270800-226271800	Active TSS	Lung	lung
47	chr1:226270800-226271800	Active TSS	Ovary	ovary
48	chr1:226270800-226271800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr1:226270800-226271800	Active TSS	Right Ventricle	heart
50	chr1:226270800-226271800	Active TSS	Sigmoid Colon	Sigmoid Colon

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