Variant report

Variant	rs4653972
Chromosome Location	chr1:224301110-224301111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr1:224301078-224302772	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224300829..224303053-chr1:224369472..224372249,3	K562	blood:
2	chr1:224295165..224298323-chr1:224300188..224302946,3	K562	blood:
3	chr1:224299141..224303224-chr1:224514971..224520507,6	MCF-7	breast:
4	chr1:224300372..224302965-chr1:224620010..224622203,2	K562	blood:
5	chr1:224300672..224304210-chr1:224370293..224374026,4	K562	blood:
6	chr1:224293723..224297684-chr1:224300401..224303649,6	MCF-7	breast:
7	chr1:224293087..224298288-chr1:224299905..224302120,6	K562	blood:

No data

Variant related genes	Relation type
FBXO28	TF binding region
ENSG00000143753	Chromatin interaction
ENSG00000252484	Chromatin interaction
ENSG00000162923	Chromatin interaction
ENSG00000143748	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10753454	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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];0.92[ASN][1000 genomes]
rs10799505	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916301	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916307	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916355	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916367	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916371	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916403	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916415	0.82[ASN][1000 genomes]
rs11808787	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049583	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12070670	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12076788	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12563153	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12730611	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13374070	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1492694	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16844819	0.82[ASN][1000 genomes]
rs17560970	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1826421	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2014782	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2048997	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2051105	0.81[ASN][1000 genomes]
rs2172361	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896985	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3767730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820483	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653563	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653564	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653986	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653991	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55664906	0.81[EUR][1000 genomes]
rs55736782	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61827699	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426139	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426143	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6426169	0.84[ASN][1000 genomes]
rs66506223	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657467	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658494	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659234	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682551	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685405	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685783	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6688818	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6690695	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691405	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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];0.99[ASN][1000 genomes]
rs7511895	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7518839	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7524705	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7526252	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7531891	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7542293	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7546235	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8328	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs869945	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs908795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997296	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs997297	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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
rs4653972	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4653972	FBXO28	cis	multi-tissue	Pritchard
rs4653972	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224291600-224301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224294600-224301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:224294600-224301400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:224294800-224301200	Weak transcription	Stomach Mucosa	stomach
5	chr1:224298200-224301200	Weak transcription	Right Atrium	heart
6	chr1:224300600-224301400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:224300800-224301200	Enhancers	Primary B cells from cord blood	blood
8	chr1:224300800-224301200	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:224300800-224301200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:224300800-224301200	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:224300800-224301200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr1:224300800-224301200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:224300800-224301200	Enhancers	K562	blood
14	chr1:224300800-224301400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:224300800-224301400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:224300800-224301400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:224301000-224301200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:224301000-224301200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr1:224301000-224301200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:224301000-224301200	Enhancers	Primary T cells from cord blood	blood
21	chr1:224301000-224301200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:224301000-224301200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr1:224301000-224301200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr1:224301000-224301200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:224301000-224301200	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:224301000-224301200	Enhancers	Dnd41	blood
27	chr1:224301000-224301200	Enhancers	GM12878-XiMat	blood
28	chr1:224301000-224301200	Enhancers	HUVEC	blood vessel
29	chr1:224301000-224301200	Enhancers	NHEK	skin
30	chr1:224301000-224301400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr1:224301000-224301400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:224301000-224301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:224301000-224301600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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