Variant report

Variant	rs2280291
Chromosome Location	chr1:224302230-224302231
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: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	chr1:224301465..224303000-chr1:224620703..224623446,2	K562	blood:
2	chr1:224301568..224304233-chr1:224516678..224521021,7	MCF-7	breast:
3	chr1:224301633..224302309-chr15:66648476..66649133,2	Hela-S3	cervix:
4	chr1:224300829..224303053-chr1:224369472..224372249,3	K562	blood:
5	chr1:224295165..224298323-chr1:224300188..224302946,3	K562	blood:
6	chr1:224299141..224303224-chr1:224514971..224520507,6	MCF-7	breast:
7	chr1:224301735..224302364-chr6:151668046..151668566,2	MCF-7	breast:
8	chr1:224301937..224302708-chr6:27115017..27115572,2	Hela-S3	cervix:
9	chr1:224300372..224302965-chr1:224620010..224622203,2	K562	blood:
10	chr1:224300672..224304210-chr1:224370293..224374026,4	K562	blood:
11	chr1:224301518..224303239-chr1:224517881..224519939,3	K562	blood:
12	chr1:224293723..224297684-chr1:224300401..224303649,6	MCF-7	breast:
13	chr1:224301888..224304582-chr1:224366795..224368300,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143748	Chromatin interaction
ENSG00000075131	Chromatin interaction
ENSG00000252484	Chromatin interaction
ENSG00000143786	Chromatin interaction
ENSG00000238939	Chromatin interaction
ENSG00000201898	Chromatin interaction
ENSG00000162923	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10753454	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799478	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10799480	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799505	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916301	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916307	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916355	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916367	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916371	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916403	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916415	0.83[ASN][1000 genomes]
rs11808787	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12038372	0.81[ASN][1000 genomes]
rs12049583	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12070670	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12076788	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12563153	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730611	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13374070	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1492694	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16844819	0.83[ASN][1000 genomes]
rs17560970	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1826421	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2014782	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2048997	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2051105	0.82[ASN][1000 genomes]
rs2172361	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2896985	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820483	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653563	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653564	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653986	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653991	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55664906	0.81[EUR][1000 genomes]
rs55736782	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827699	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426139	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426143	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426169	0.85[ASN][1000 genomes]
rs66506223	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6657467	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658494	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659234	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682551	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685405	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685783	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6688818	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6690695	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6691405	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698041	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6700284	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7511895	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7518839	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7524705	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7526252	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7531891	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7542293	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7546235	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8328	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs869945	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs908795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997296	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs997297	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873222	chr1:224292898-224335422	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2280291	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs2280291	FBXO28	cis	multi-tissue	Pritchard
rs2280291	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224301200-224302400	Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:224301200-224302400	Active TSS	Liver	Liver
3	chr1:224301200-224302400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
4	chr1:224301200-224302600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:224301200-224302600	Active TSS	Brain Angular Gyrus	brain
6	chr1:224301200-224302600	Active TSS	Brain Anterior Caudate	brain
7	chr1:224301200-224302600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr1:224301200-224302600	Active TSS	Osteobl	bone
9	chr1:224301200-224302800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:224301200-224302800	Active TSS	Brain Substantia Nigra	brain
11	chr1:224301200-224303000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:224301200-224303000	Active TSS	Brain Hippocampus Middle	brain
13	chr1:224301200-224303000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr1:224301200-224303000	Active TSS	Fetal Brain Female	brain
15	chr1:224301200-224303000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr1:224301200-224303000	Active TSS	A549	lung
17	chr1:224301200-224303200	Active TSS	Stomach Smooth Muscle	stomach
18	chr1:224301200-224303400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:224301200-224303600	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr1:224301200-224304000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:224301200-224304000	Active TSS	NHLF	lung
22	chr1:224301200-224304400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:224301200-224304400	Active TSS	Right Atrium	heart
24	chr1:224301400-224302400	Active TSS	Primary B cells from peripheral blood	blood
25	chr1:224301400-224302400	Active TSS	Primary T cells fromperipheralblood	blood
26	chr1:224301400-224302400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr1:224301400-224302400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:224301400-224302400	Active TSS	Colon Smooth Muscle	Colon
29	chr1:224301400-224302400	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:224301400-224302400	Bivalent/Poised TSS	HepG2	liver
31	chr1:224301400-224302600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:224301400-224302600	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:224301400-224302600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:224301400-224302600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:224301400-224302600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:224301400-224302600	Active TSS	Fetal Brain Male	brain
37	chr1:224301400-224302600	Active TSS	Fetal Stomach	stomach
38	chr1:224301400-224302600	Active TSS	Thymus	Thymus
39	chr1:224301400-224302800	Active TSS	Aorta	Aorta
40	chr1:224301400-224302800	Active TSS	Fetal Muscle Trunk	muscle
41	chr1:224301400-224302800	Active TSS	Psoas Muscle	Psoas
42	chr1:224301400-224302800	Active TSS	Right Ventricle	heart
43	chr1:224301400-224302800	Active TSS	Stomach Mucosa	stomach
44	chr1:224301400-224302800	Active TSS	HSMM	muscle
45	chr1:224301400-224303000	Active TSS	Brain Cingulate Gyrus	brain
46	chr1:224301400-224303000	Active TSS	Colonic Mucosa	Colon
47	chr1:224301400-224303000	Active TSS	Fetal Muscle Leg	muscle
48	chr1:224301400-224303000	Active TSS	Placenta	Placenta
49	chr1:224301400-224303000	Active TSS	Fetal Thymus	thymus
50	chr1:224301400-224303000	Active TSS	Ovary	ovary

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