Variant report

Variant	rs7543135
Chromosome Location	chr1:226272178-226272179
allele	G/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	chr1:226248851..226254336-chr1:226269112..226274282,12	MCF-7	breast:
3	chr1:226248789..226253333-chr1:226269675..226273948,8	MCF-7	breast:
4	chr1:226270770..226272699-chr1:226374583..226377096,2	MCF-7	breast:
5	chr1:226185497..226187877-chr1:226269946..226272750,2	MCF-7	breast:

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

Extended variants
information (count: 20 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10799335	0.85[EUR][1000 genomes]
rs10915930	0.89[EUR][1000 genomes]
rs10915931	0.89[EUR][1000 genomes]
rs10915932	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060155	0.92[EUR][1000 genomes]
rs12066979	0.92[EUR][1000 genomes]
rs12086044	0.84[EUR][1000 genomes]
rs12096468	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12096737	0.93[EUR][1000 genomes]
rs12117683	0.83[AFR][1000 genomes]
rs3768543	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4271181	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678547	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6679192	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6681021	0.89[EUR][1000 genomes]
rs6692329	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6692849	0.92[EUR][1000 genomes]
rs6700189	0.86[AMR][1000 genomes];0.88[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7543135	H3F3A	cis	Esophagus Muscularis	GTEx
rs7543135	H3F3A	cis	Adipose Subcutaneous	GTEx
rs7543135	H3F3A	cis	Esophagus Mucosa	GTEx
rs7543135	H3F3A	cis	Muscle Skeletal	GTEx
rs7543135	H3F3A	cis	Whole Blood	GTEx
rs7543135	H3F3A	cis	Artery Aorta	GTEx
rs7543135	H3F3A	cis	Nerve Tibial	GTEx
rs7543135	H3F3A	cis	Artery Tibial	GTEx
rs7543135	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs7543135	H3F3A	cis	Heart Left Ventricle	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226271800-226272200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr1:226271800-226272400	Weak transcription	Stomach Mucosa	stomach
3	chr1:226271800-226277000	Weak transcription	K562	blood
4	chr1:226271800-226286200	Weak transcription	Ovary	ovary
5	chr1:226271800-226288000	Weak transcription	Right Atrium	heart
6	chr1:226271800-226288400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:226272000-226272400	Weak transcription	GM12878-XiMat	blood
8	chr1:226272000-226273600	Enhancers	Primary B cells from cord blood	blood
9	chr1:226272000-226273600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:226272000-226273600	Weak transcription	Pancreas	Pancrea
11	chr1:226272000-226273600	Weak transcription	Spleen	Spleen
12	chr1:226272000-226274000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:226272000-226274200	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:226272000-226274600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:226272000-226275400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:226272000-226276400	Weak transcription	Placenta	Placenta
17	chr1:226272000-226276800	Weak transcription	Colonic Mucosa	Colon
18	chr1:226272000-226281000	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:226272000-226282200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:226272000-226285400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:226272000-226287800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:226272000-226288200	Weak transcription	H9 Cell Line	embryonic stem cell

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