Variant report

Variant	rs10799335
Chromosome Location	chr1:226261267-226261268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226132398..226133993-chr1:226259835..226261737,2	K562	blood:
2	chr1:226252587..226254358-chr1:226261126..226263973,2	MCF-7	breast:
3	chr1:226252549..226256033-chr1:226258651..226261482,3	MCF-7	breast:
4	chr1:226258835..226263842-chr1:226306097..226310860,6	K562	blood:
5	chr1:226259780..226262512-chr1:226298395..226301346,2	K562	blood:
6	chr1:226259247..226261395-chr1:226295322..226298055,2	MCF-7	breast:
7	chr1:226248786..226251672-chr1:226260844..226263212,2	MCF-7	breast:
8	chr1:226186269..226188248-chr1:226260401..226263300,2	K562	blood:
9	chr1:226260970..226263013-chr1:226283017..226285743,2	K562	blood:
10	chr1:226260420..226263013-chr1:226284243..226287339,3	K562	blood:
11	chr1:226248158..226251632-chr1:226261132..226264473,3	MCF-7	breast:
12	chr1:226260259..226262161-chr1:226354959..226356498,2	K562	blood:
13	chr1:226260174..226262494-chr11:65265384..65267097,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10915930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915931	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915932	0.87[EUR][1000 genomes]
rs12060155	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12066979	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12086044	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096388	0.83[AFR][1000 genomes]
rs12096468	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096737	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4271181	0.85[CHB][hapmap];0.93[EUR][1000 genomes]
rs6426106	0.92[JPT][hapmap]
rs6678547	0.94[EUR][1000 genomes]
rs6681021	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692329	0.86[EUR][1000 genomes]
rs6692849	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543135	0.85[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10799335	H3F3A	cis	Artery Tibial	GTEx
rs10799335	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs10799335	H3F3A	cis	Esophagus Mucosa	GTEx
rs10799335	H3F3A	cis	Muscle Skeletal	GTEx
rs10799335	H3F3A	cis	Nerve Tibial	GTEx
rs10799335	H3F3A	cis	Adipose Subcutaneous	GTEx
rs10799335	H3F3A	cis	Artery Aorta	GTEx

Chromatin state (count:124 , 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	chr1:226253200-226270400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:226253200-226270600	Weak transcription	Aorta	Aorta
4	chr1:226253400-226263000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:226253400-226263200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr1:226253400-226263400	Strong transcription	Placenta	Placenta
7	chr1:226253600-226261800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:226253600-226263400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:226253600-226270400	Weak transcription	Small Intestine	intestine
10	chr1:226254000-226267400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:226254400-226263000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:226254600-226261400	Strong transcription	Fetal Intestine Large	intestine
13	chr1:226254600-226261800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr1:226254600-226261800	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr1:226254600-226261800	Strong transcription	HSMM	muscle
16	chr1:226254600-226262000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:226254600-226262600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:226254600-226262600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:226254600-226262800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:226254600-226262800	Strong transcription	Osteobl	bone
21	chr1:226254600-226263000	Strong transcription	HUVEC	blood vessel
22	chr1:226254600-226263200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:226254600-226263600	Strong transcription	Adipose Nuclei	Adipose
24	chr1:226254600-226263800	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:226254600-226266000	Weak transcription	Psoas Muscle	Psoas
26	chr1:226254600-226270400	Weak transcription	Right Ventricle	heart
27	chr1:226254800-226262000	Strong transcription	Fetal Brain Female	brain
28	chr1:226254800-226262400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:226254800-226262600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:226254800-226263600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:226255000-226261600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:226255000-226261800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:226255000-226262000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:226255000-226262600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:226255200-226262600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:226255200-226262600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:226255400-226263000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:226255400-226263200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:226255600-226261800	Strong transcription	Fetal Kidney	kidney
40	chr1:226256000-226261800	Strong transcription	Brain Hippocampus Middle	brain
41	chr1:226256200-226263400	Strong transcription	Liver	Liver
42	chr1:226256400-226262000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:226256400-226262600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:226256400-226262800	Strong transcription	Fetal Lung	lung
45	chr1:226256600-226261800	Strong transcription	K562	blood
46	chr1:226256600-226262000	Strong transcription	A549	lung
47	chr1:226256600-226262800	Strong transcription	Dnd41	blood
48	chr1:226256600-226263200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:226256600-226263400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:226256600-226263800	Strong transcription	Fetal Thymus	thymus

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