Variant report

Variant	rs7688984
Chromosome Location	chr4:15657253-15657254
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr4:15656256-15657596	K562	blood:	n/a	chr4:15656680-15656694 chr4:15656727-15656738 chr4:15656730-15656744 chr4:15657321-15657333 chr4:15656621-15656630 chr4:15656729-15656743 chr4:15657480-15657491
2	USF2	chr4:15656803-15657450	GM12878	blood:	n/a	chr4:15657092-15657103
3	YY1	chr4:15656700-15657648	A549	lung:	n/a	chr4:15656727-15656738 chr4:15656730-15656744 chr4:15657321-15657333 chr4:15656729-15656743 chr4:15657480-15657491
4	POLR2A	chr4:15656670-15657484	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:15656283-15658011	Raji	blood:	n/a	n/a
6	TAF7	chr4:15656224-15657979	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAFK	chr4:15657076-15657591	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr4:15656737-15657570	MCF-7	breast:	n/a	chr4:15657135-15657145 chr4:15657091-15657100 chr4:15657092-15657103 chr4:15657093-15657102 chr4:15657091-15657106
9	POLR2A	chr4:15656638-15657891	SK-N-SH	brain:	n/a	n/a
10	ZNF384	chr4:15657079-15657285	GM12878	blood:	n/a	n/a
11	YY1	chr4:15656677-15657682	SK-N-SH	brain:	n/a	chr4:15656680-15656694 chr4:15656727-15656738 chr4:15656730-15656744 chr4:15657321-15657333 chr4:15656729-15656743 chr4:15657480-15657491
12	POU2F2	chr4:15656962-15657524	GM12891	blood:	n/a	chr4:15657366-15657378
13	MXI1	chr4:15656213-15657376	GM12878	blood:	n/a	chr4:15657094-15657103
14	POU2F2	chr4:15657035-15657392	GM12878	blood:	n/a	chr4:15657366-15657378
15	RELA	chr4:15656722-15657543	GM15510	blood:	n/a	n/a
16	JUND	chr4:15656842-15658077	H1-hESC	embryonic stem cell:	n/a	chr4:15657445-15657459
17	E2F4	chr4:15656485-15657278	K562	blood:	n/a	chr4:15656733-15656742 chr4:15657131-15657143 chr4:15656988-15656997 chr4:15656984-15656993
18	POLR2A	chr4:15656210-15657834	MCF10A-Er-Src	breast:	n/a	n/a
19	BCL3	chr4:15656555-15657319	GM12878	blood:	n/a	chr4:15656617-15656630 chr4:15656667-15656680 chr4:15656648-15656661 chr4:15656729-15656742
20	NFATC1	chr4:15656975-15657527	GM12878	blood:	n/a	n/a
21	BCL3	chr4:15656632-15657493	A549	lung:	n/a	chr4:15656667-15656680 chr4:15656648-15656661 chr4:15656729-15656742
22	PML	chr4:15656699-15657429	MCF-7	breast:	n/a	n/a
23	MAZ	chr4:15655158-15657667	K562	blood:	n/a	chr4:15657135-15657145 chr4:15657091-15657100 chr4:15657092-15657103 chr4:15657093-15657102 chr4:15657091-15657106
24	YY1	chr4:15656525-15657631	SK-N-SH_RA	brain:	n/a	chr4:15656680-15656694 chr4:15656727-15656738 chr4:15656730-15656744 chr4:15657321-15657333 chr4:15656621-15656630 chr4:15656729-15656743 chr4:15657480-15657491
25	REST	chr4:15656581-15657531	HL-60	blood:	n/a	chr4:15657259-15657277 chr4:15656791-15656804
26	HA-E2F1	chr4:15656435-15657426	Hela-S3	cervix:	n/a	chr4:15656733-15656742 chr4:15657131-15657143 chr4:15656988-15656997 chr4:15656984-15656993
27	USF1	chr4:15656840-15657402	SK-N-SH_RA	brain:	n/a	n/a
28	REST	chr4:15655634-15657879	H1-neurons	neurons:	n/a	chr4:15657259-15657277 chr4:15656362-15656375 chr4:15656791-15656804
29	E2F6	chr4:15656367-15657938	K562	blood:	n/a	chr4:15657782-15657789 chr4:15657565-15657575 chr4:15656733-15656742 chr4:15657800-15657817 chr4:15657131-15657143 chr4:15657581-15657590 chr4:15656988-15656997 chr4:15657130-15657141 chr4:15657587-15657597 chr4:15656984-15656993 chr4:15657782-15657789 chr4:15657782-15657789
30	CCNT2	chr4:15656329-15658018	K562	blood:	n/a	chr4:15657746-15657755 chr4:15657603-15657612
31	SP1	chr4:15656906-15657326	GM12878	blood:	n/a	chr4:15657134-15657143 chr4:15657132-15657144 chr4:15657133-15657147
32	POLR2A	chr4:15656570-15657449	A549	lung:	n/a	n/a
33	POLR2A	chr4:15656197-15658025	GM18505	blood:	n/a	n/a
34	POLR2A	chr4:15656070-15657503	H1-neurons	neurons:	n/a	n/a
35	CHD1	chr4:15656349-15657479	GM12878	blood:	n/a	n/a
36	POLR2A	chr4:15656713-15657365	K562	blood:	n/a	n/a
37	POLR2A	chr4:15656200-15657889	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr4:15656486-15657671	HCT-116	colon:	n/a	n/a
39	USF1	chr4:15656843-15657365	K562	blood:	n/a	n/a
40	E2F6	chr4:15656856-15657484	K562	blood:	n/a	chr4:15657131-15657143 chr4:15656988-15656997 chr4:15657130-15657141 chr4:15656984-15656993
41	MAX	chr4:15656740-15657597	SK-N-SH	brain:	n/a	chr4:15657135-15657145 chr4:15657091-15657100 chr4:15657092-15657103 chr4:15657093-15657102 chr4:15657091-15657106
42	POLR2A	chr4:15656252-15657826	GM15510	blood:	n/a	n/a
43	BHLHE40	chr4:15656620-15657421	K562	blood:	n/a	chr4:15656721-15656737 chr4:15656728-15656744 chr4:15656683-15656699
44	YY1	chr4:15656765-15657513	HepG2	liver:	n/a	chr4:15657321-15657333 chr4:15657480-15657491
45	TAF1	chr4:15656238-15658112	H1-hESC	embryonic stem cell:	n/a	n/a
46	EP300	chr4:15656925-15657291	K562	blood:	n/a	n/a
47	POLR2A	chr4:15656658-15658363	U87	brain:	n/a	n/a
48	TAF1	chr4:15657034-15657316	GM12892	blood:	n/a	n/a
49	POLR2A	chr4:15655492-15658152	HUVEC	blood vessel:	n/a	n/a
50	TAF1	chr4:15656751-15657344	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
2	chr4:15654775..15659231-chr4:15659761..15666940,9	K562	blood:
3	chr4:15002808..15006132-chr4:15656406..15658114,3	K562	blood:
4	chr4:15655671..15658131-chr4:15716646..15719360,2	MCF-7	breast:
5	chr4:15479740..15482605-chr4:15655501..15658427,3	MCF-7	breast:
6	chr4:15469326..15470996-chr4:15657243..15660173,2	MCF-7	breast:
7	chr4:15656159..15658615-chr4:15712805..15714316,2	K562	blood:
8	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:
9	chr4:15654963..15657954-chr4:15685988..15688544,3	MCF-7	breast:
10	chr21:34601586..34602556-chr4:15656823..15657778,2	NB4	blood:
11	chr12:122235040..122237798-chr4:15655451..15658367,2	MCF-7	breast:
12	chr4:15655595..15658742-chr4:15680185..15687360,10	MCF-7	breast:
13	chr4:15652080..15658606-chr4:15677363..15685579,17	MCF-7	breast:

Variant related genes	Relation type
FBXL5	TF binding region
ENSG00000048342	Chromatin interaction
ENSG00000159110	Chromatin interaction
ENSG00000237765	Chromatin interaction
ENSG00000109743	Chromatin interaction
ENSG00000137449	Chromatin interaction
ENSG00000118564	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000247624	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10008376	0.94[EUR][1000 genomes]
rs10008975	0.94[EUR][1000 genomes]
rs10214	0.94[EUR][1000 genomes]
rs11728084	0.92[EUR][1000 genomes]
rs12499412	0.95[EUR][1000 genomes]
rs12500587	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12500770	0.92[EUR][1000 genomes]
rs12512883	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12644655	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12651550	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13110674	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13120905	0.95[EUR][1000 genomes]
rs13129739	0.89[EUR][1000 genomes]
rs13147590	0.95[EUR][1000 genomes]
rs1789	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35414597	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235379	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4270584	0.90[EUR][1000 genomes]
rs4358397	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4382032	0.88[ASN][1000 genomes]
rs4453929	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4470622	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4524378	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4557256	0.94[EUR][1000 genomes]
rs4616746	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4631041	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4698402	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698404	0.95[EUR][1000 genomes]
rs4698406	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4698407	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698409	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61021642	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6414765	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6414767	0.95[EUR][1000 genomes]
rs6449153	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6850169	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6850422	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7438356	0.94[EUR][1000 genomes]
rs7662032	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7685083	0.95[EUR][1000 genomes]
rs7687003	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7690362	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7696127	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7696938	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8180240	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9997068	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3322833	chr4:15655679-15658227	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3351978	chr4:15655904-15658002	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7688984	FBXL5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15653400-15657600	Active TSS	Right Atrium	heart
2	chr4:15653800-15657600	Active TSS	K562	blood
3	chr4:15654400-15657400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:15654600-15657600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:15654600-15658000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:15654600-15658200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:15654800-15657400	Active TSS	Brain Hippocampus Middle	brain
8	chr4:15654800-15657600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:15654800-15657600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:15654800-15657600	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr4:15654800-15657600	Active TSS	GM12878-XiMat	blood
12	chr4:15654800-15658000	Active TSS	Psoas Muscle	Psoas
13	chr4:15655000-15657400	Active TSS	Brain Cingulate Gyrus	brain
14	chr4:15655000-15657600	Active TSS	Aorta	Aorta
15	chr4:15655000-15657800	Active TSS	Left Ventricle	heart
16	chr4:15655000-15657800	Active TSS	Right Ventricle	heart
17	chr4:15655000-15658000	Active TSS	Ovary	ovary
18	chr4:15655200-15657400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:15655200-15657600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr4:15655200-15657800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr4:15655600-15657400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:15655600-15657400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:15655600-15657400	Active TSS	Lung	lung
24	chr4:15655600-15657600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:15655600-15657600	Active TSS	Brain Angular Gyrus	brain
26	chr4:15655600-15657600	Active TSS	Brain Germinal Matrix	brain
27	chr4:15655600-15657600	Active TSS	Fetal Stomach	stomach
28	chr4:15655600-15657600	Active TSS	Rectal Smooth Muscle	rectum
29	chr4:15655600-15657800	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr4:15655600-15657800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:15655600-15657800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:15655600-15657800	Active TSS	Brain Substantia Nigra	brain
33	chr4:15655600-15657800	Active TSS	Gastric	stomach
34	chr4:15655600-15657800	Active TSS	HSMMtube	muscle
35	chr4:15655600-15658200	Active TSS	H9 Cell Line	embryonic stem cell
36	chr4:15655600-15658200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr4:15655800-15657400	Active TSS	Fetal Intestine Small	intestine
38	chr4:15655800-15657400	Active TSS	Pancreas	Pancrea
39	chr4:15655800-15657400	Active TSS	Stomach Mucosa	stomach
40	chr4:15655800-15657600	Active TSS	Fetal Intestine Large	intestine
41	chr4:15655800-15657600	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr4:15655800-15657600	Active TSS	Thymus	Thymus
43	chr4:15655800-15657800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:15655800-15657800	Active TSS	Colon Smooth Muscle	Colon
45	chr4:15655800-15657800	Active TSS	Fetal Lung	lung
46	chr4:15655800-15658000	Active TSS	Esophagus	oesophagus
47	chr4:15655800-15658200	Active TSS	Duodenum Mucosa	Duodenum
48	chr4:15655800-15658400	Active TSS	Brain Anterior Caudate	brain
49	chr4:15656000-15657600	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr4:15656000-15657600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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