Variant report

Variant	rs10915931
Chromosome Location	chr1:226267753-226267754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226257154..226258738-chr1:226266195..226268284,2	MCF-7	breast:
2	chr1:226248291..226251598-chr1:226265940..226269006,3	MCF-7	breast:
3	chr1:226265249..226269175-chr1:226308279..226312105,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10753411	0.84[AFR][1000 genomes]
rs10799335	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915930	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915932	0.92[EUR][1000 genomes]
rs12060155	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12066979	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12086044	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096468	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096737	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768543	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4271181	0.97[EUR][1000 genomes]
rs6678547	0.95[EUR][1000 genomes]
rs6681021	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692329	0.90[EUR][1000 genomes]
rs6692849	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700189	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543135	0.89[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
rs10915931	H3F3A	cis	Adipose Subcutaneous	GTEx
rs10915931	H3F3A	cis	Whole Blood	GTEx
rs10915931	H3F3A	cis	Artery Tibial	GTEx
rs10915931	H3F3A	cis	Esophagus Muscularis	GTEx
rs10915931	H3F3A	cis	Muscle Skeletal	GTEx
rs10915931	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs10915931	H3F3A	cis	Artery Aorta	GTEx
rs10915931	H3F3A	cis	Esophagus Mucosa	GTEx
rs10915931	H3F3A	cis	Nerve Tibial	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226253000-226270400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:226253200-226270400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:226253200-226270600	Weak transcription	Aorta	Aorta
4	chr1:226253600-226270400	Weak transcription	Small Intestine	intestine
5	chr1:226254600-226270400	Weak transcription	Right Ventricle	heart
6	chr1:226256600-226270400	Weak transcription	Pancreas	Pancrea
7	chr1:226256600-226270600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:226257800-226270400	Weak transcription	Stomach Mucosa	stomach
9	chr1:226258000-226270400	Weak transcription	Ovary	ovary
10	chr1:226258000-226270400	Weak transcription	NHEK	skin
11	chr1:226258000-226270600	Weak transcription	Lung	lung
12	chr1:226258200-226270400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:226258200-226270400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:226258600-226270400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:226258600-226270400	Weak transcription	Esophagus	oesophagus
16	chr1:226258800-226270400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:226258800-226270600	Weak transcription	Gastric	stomach
18	chr1:226259000-226270400	Weak transcription	Brain Germinal Matrix	brain
19	chr1:226259200-226270400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:226259200-226270400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:226260000-226270400	Weak transcription	Brain Angular Gyrus	brain
22	chr1:226260000-226270600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:226260400-226270200	Weak transcription	Hela-S3	cervix
24	chr1:226260400-226270400	Weak transcription	Colonic Mucosa	Colon
25	chr1:226260600-226270200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:226260600-226270400	Weak transcription	Brain Anterior Caudate	brain
27	chr1:226260600-226270400	Weak transcription	Brain Substantia Nigra	brain
28	chr1:226260600-226270400	Weak transcription	NHLF	lung
29	chr1:226260800-226270600	Weak transcription	Fetal Brain Male	brain
30	chr1:226261000-226270400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:226261000-226270400	Weak transcription	HMEC	breast
32	chr1:226261200-226270200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:226261200-226270200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:226261200-226270200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:226261200-226270200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:226261200-226270400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:226261200-226270400	Weak transcription	NH-A	brain
38	chr1:226261200-226270600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:226261400-226270400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:226261600-226270200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:226261600-226270400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:226261600-226270400	Weak transcription	NHDF-Ad	bronchial
43	chr1:226261800-226270200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:226261800-226270200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:226261800-226270200	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:226261800-226270400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:226261800-226270400	Weak transcription	HSMM	muscle
48	chr1:226262000-226268000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:226262000-226270200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:226262000-226270400	Weak transcription	Fetal Brain Female	brain

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