Variant report

Variant	rs12096468
Chromosome Location	chr1:226258270-226258271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226186633..226189098-chr1:226257320..226260557,3	K562	blood:
2	chr1:226183330..226185192-chr1:226257452..226258976,2	K562	blood:
3	chr1:226257154..226258738-chr1:226266195..226268284,2	MCF-7	breast:
4	chr1:226256658..226258730-chr1:226270014..226271766,2	MCF-7	breast:
5	chr1:226257129..226259171-chr1:226296635..226298571,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225518	Chromatin interaction
ENSG00000143751	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10799335	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915930	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915931	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915932	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12060155	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12066979	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12086044	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096737	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768543	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4271181	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6678547	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6681021	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692329	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6692849	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700189	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7543135	0.86[AMR][1000 genomes];0.87[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12096468	H3F3A	cis	Nerve Tibial	GTEx
rs12096468	H3F3A	cis	Artery Tibial	GTEx
rs12096468	H3F3A	cis	Muscle Skeletal	GTEx
rs12096468	H3F3A	cis	Whole Blood	GTEx
rs12096468	H3F3A	cis	Artery Aorta	GTEx
rs12096468	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs12096468	H3F3A	cis	Esophagus Mucosa	GTEx
rs12096468	H3F3A	cis	Thyroid	GTEx
rs12096468	H3F3A	cis	Esophagus Muscularis	GTEx
rs12096468	H3F3A	cis	lung	GTEx
rs12096468	H3F3A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226253000-226270400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:226253200-226258800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
3	chr1:226253200-226260200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:226253200-226270400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:226253200-226270600	Weak transcription	Aorta	Aorta
6	chr1:226253400-226259200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:226253400-226263000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:226253400-226263200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:226253400-226263400	Strong transcription	Placenta	Placenta
10	chr1:226253600-226260200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:226253600-226261800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:226253600-226263400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:226253600-226270400	Weak transcription	Small Intestine	intestine
14	chr1:226253800-226260600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:226254000-226258800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:226254000-226258800	Strong transcription	Spleen	Spleen
17	chr1:226254000-226267400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:226254200-226260600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr1:226254200-226261200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:226254400-226259000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:226254400-226263000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:226254600-226258600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:226254600-226258800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:226254600-226258800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:226254600-226259000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:226254600-226259000	Strong transcription	HepG2	liver
27	chr1:226254600-226259600	Weak transcription	Fetal Brain Male	brain
28	chr1:226254600-226259800	Weak transcription	Colonic Mucosa	Colon
29	chr1:226254600-226259800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr1:226254600-226260400	Strong transcription	Hela-S3	cervix
31	chr1:226254600-226260600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:226254600-226261200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:226254600-226261200	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:226254600-226261200	Strong transcription	NH-A	brain
35	chr1:226254600-226261400	Strong transcription	Fetal Intestine Large	intestine
36	chr1:226254600-226261800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:226254600-226261800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:226254600-226261800	Strong transcription	HSMM	muscle
39	chr1:226254600-226262000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:226254600-226262600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:226254600-226262600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:226254600-226262800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:226254600-226262800	Strong transcription	Osteobl	bone
44	chr1:226254600-226263000	Strong transcription	HUVEC	blood vessel
45	chr1:226254600-226263200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:226254600-226263600	Strong transcription	Adipose Nuclei	Adipose
47	chr1:226254600-226263800	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:226254600-226266000	Weak transcription	Psoas Muscle	Psoas
49	chr1:226254600-226270400	Weak transcription	Right Ventricle	heart
50	chr1:226254800-226258600	Strong transcription	Fetal Stomach	stomach

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