Variant report

Variant	rs6426099
Chromosome Location	chr1:226247741-226247742
allele	C/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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
2	chr1:226247680..226258196-chr1:226306136..226315725,36	MCF-7	breast:
3	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
4	chr1:226184876..226191468-chr1:226247585..226254254,12	MCF-7	breast:
5	chr1:226217322..226219957-chr1:226246181..226248260,3	K562	blood:
6	chr1:226213068..226214895-chr1:226247410..226249127,2	K562	blood:
7	chr1:226203662..226205459-chr1:226246341..226248870,2	MCF-7	breast:
8	chr1:226247090..226249451-chr1:226292552..226294249,2	K562	blood:
9	chr1:226246636..226248213-chr1:226248216..226249940,2	MCF-7	breast:
10	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf55-1	chr1:226245769-226249546	NONHSAT009869

No data

Variant related genes	Relation type
ENSG00000270598	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10157179	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10753411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799333	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10799334	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10915920	0.85[EUR][1000 genomes]
rs10915921	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915927	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12128917	0.89[EUR][1000 genomes]
rs1877158	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2001307	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4477241	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4604663	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653438	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653439	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653703	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653704	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653705	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426096	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6426098	0.98[EUR][1000 genomes]
rs6675606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693325	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6701318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73100558	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7550220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7553984	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9701639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6426099	H3F3A	cis	Artery Tibial	GTEx
rs6426099	H3F3A	cis	Esophagus Mucosa	GTEx
rs6426099	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs6426099	H3F3A	cis	Nerve Tibial	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226222600-226248600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:226226000-226248000	Weak transcription	Left Ventricle	heart
3	chr1:226229600-226248200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:226229800-226249400	Weak transcription	Spleen	Spleen
5	chr1:226230000-226249200	Weak transcription	Aorta	Aorta
6	chr1:226231200-226249200	Weak transcription	Pancreas	Pancrea
7	chr1:226232000-226249200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:226232200-226249400	Weak transcription	Gastric	stomach
9	chr1:226232600-226248600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:226234600-226248000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:226234600-226248800	Weak transcription	HSMM	muscle
12	chr1:226234800-226248800	Weak transcription	HSMMtube	muscle
13	chr1:226235000-226248200	Weak transcription	Fetal Intestine Large	intestine
14	chr1:226235000-226248800	Weak transcription	Colonic Mucosa	Colon
15	chr1:226235200-226248600	Weak transcription	HepG2	liver
16	chr1:226235200-226249200	Weak transcription	Small Intestine	intestine
17	chr1:226235400-226248000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:226235400-226248600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:226235400-226249200	Weak transcription	Esophagus	oesophagus
20	chr1:226235600-226248200	Weak transcription	Fetal Intestine Small	intestine
21	chr1:226235800-226248200	Weak transcription	Stomach Mucosa	stomach
22	chr1:226236200-226248200	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:226236200-226248600	Weak transcription	Fetal Brain Male	brain
24	chr1:226236800-226248200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:226236800-226248600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:226237200-226248600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:226237600-226248800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:226238400-226248200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:226238600-226249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:226240000-226248400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:226240800-226247800	Weak transcription	Psoas Muscle	Psoas
32	chr1:226241000-226249200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:226241200-226248200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:226242400-226248200	Weak transcription	Fetal Heart	heart
35	chr1:226242400-226248400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:226242400-226249200	Weak transcription	Lung	lung
37	chr1:226242600-226248600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:226242600-226248600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:226242600-226248800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:226242800-226248200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:226242800-226248200	Weak transcription	Fetal Brain Female	brain
42	chr1:226242800-226248400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:226242800-226248600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:226242800-226248600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:226242800-226248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:226242800-226248800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:226242800-226248800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:226242800-226249000	Weak transcription	Ovary	ovary
49	chr1:226242800-226249200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:226243000-226248600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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