Variant report

Variant	rs6687334
Chromosome Location	chr1:224300723-224300724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
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	POLR2A	chr1:224300703-224300776	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:224300718-224300768	H1-hESC	embryonic stem cell:	embryo
2	chr1:224300718-224300768	ProgFib	skin:	n/a
3	chr1:224300718-224300768	SK-N-SH	brain:	n/a
4	chr1:224300718-224300768	HL-60	blood:	n/a
5	chr1:224300718-224300768	Hela-S3	cervix:	n/a
6	chr1:224300718-224300768	AG09319	gingival:	n/a
7	chr1:224300718-224300768	K562	blood:	n/a
8	chr1:224300718-224300768	BE2_C	brain:	n/a
9	chr1:224300718-224300768	Hepatocyte	liver:	n/a
10	chr1:224300718-224300768	ovcar-3	ovarian:	n/a
11	chr1:224300718-224300768	GM12892	blood:	n/a
12	chr1:224300718-224300768	PrEC	prostate:	n/a
13	chr1:224300718-224300768	ECC-1	luminal epithelium:	n/a
14	chr1:224300718-224300768	NH-A	brain:	n/a
15	chr1:224300718-224300768	HAEpiC	amniotic membrane:	n/a
16	chr1:224300718-224300768	GM19239	blood:	n/a
17	chr1:224300718-224300768	NT2-D1	testis:	n/a
18	chr1:224300718-224300768	NHDF-neo	bronchial:	n/a
19	chr1:224300718-224300768	LNCaP	prostate:	n/a
20	chr1:224300718-224300768	HNPCEpiC	eye:	n/a
21	chr1:224300718-224300768	GM06990	blood:	n/a
22	chr1:224300718-224300768	Jurkat	blood:	n/a
23	chr1:224300718-224300768	NHBE	bronchial:	n/a
24	chr1:224300718-224300768	AG10803	skin:	n/a
25	chr1:224300718-224300768	HCT-116	colon:	n/a
26	chr1:224300718-224300768	HRCEpiC	kidney:	n/a
27	chr1:224300718-224300768	PFSK-1	brain:	n/a
28	chr1:224300718-224300768	HepG2	liver:	n/a
29	chr1:224300718-224300768	HCF	heart:	n/a
30	chr1:224300718-224300768	Caco-2	colon:	n/a
31	chr1:224300718-224300768	AG04450	lung:	fetal
32	chr1:224300718-224300768	NB4	blood:	n/a
33	chr1:224300718-224300768	HRPEpiC	eye:	n/a
34	chr1:224300718-224300768	HCPEpiC	choroid plexus:	n/a
35	chr1:224300718-224300768	HMEC	breast:	n/a
36	chr1:224300718-224300768	A549	lung:	n/a
37	chr1:224300718-224300768	AoSMC	blood vessel:	n/a
38	chr1:224300718-224300768	SK-N-MC	brain:	n/a
39	chr1:224300718-224300768	IMR90	lung:	fetal
40	chr1:224300718-224300768	HUVEC	blood vessel:	n/a
41	chr1:224300718-224300768	MCF10A-Er-Src	breast:	n/a
42	chr1:224300718-224300768	SK-N-SH_RA	brain:	n/a
43	chr1:224300718-224300768	HCM	heart:	n/a
44	chr1:224300718-224300768	T-47D	breast:	n/a
45	chr1:224300718-224300768	GM12891	blood:	n/a
46	chr1:224300718-224300768	AG04449	skin:	fetal
47	chr1:224300718-224300768	BJ	skin:	n/a
48	chr1:224300718-224300768	HEEpiC	esophagus:	n/a
49	chr1:224300718-224300768	SAEC	small airway:	n/a
50	chr1:224300718-224300768	HRE	kidney:	n/a

(count:6 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10429876	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916393	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916405	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11576822	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12079996	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12144944	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2032003	0.86[EUR][1000 genomes]
rs2172358	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3754091	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3767728	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4359008	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4484894	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4528084	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56044078	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6680540	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6692443	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6687334	FBXO28	cis	multi-tissue	Pritchard
rs6687334	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr1:224297200-224301000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:224298200-224301200	Weak transcription	Right Atrium	heart
7	chr1:224300600-224300800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:224300600-224300800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:224300600-224301000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:224300600-224301000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:224300600-224301400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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