Variant report

Variant	rs6838162
Chromosome Location	chr4:76912228-76912229
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:443)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:443 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr4:76911665-76912361	K562	blood:	n/a	n/a
2	REST	chr4:76911872-76912259	SK-N-SH	brain:	n/a	n/a
3	RFX5	chr4:76911932-76912341	Hela-S3	cervix:	n/a	n/a
4	PML	chr4:76911506-76912403	GM12878	blood:	n/a	n/a
5	REST	chr4:76911776-76912446	A549	lung:	n/a	n/a
6	SP1	chr4:76911917-76912287	H1-hESC	embryonic stem cell:	n/a	chr4:76912239-76912251 chr4:76912240-76912249
7	SIN3AK20	chr4:76911835-76912255	PFSK-1	brain:	n/a	n/a
8	ELK4	chr4:76911555-76912269	Hela-S3	cervix:	n/a	chr4:76912099-76912110
9	CBX3	chr4:76911854-76912725	K562	blood:	n/a	n/a
10	POLR2A	chr4:76911771-76912430	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr4:76911699-76912281	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr4:76911824-76912331	GM15510	blood:	n/a	n/a
13	MYC	chr4:76911764-76912295	MCF-7	breast:	n/a	n/a
14	MAZ	chr4:76911919-76912350	HepG2	liver:	n/a	n/a
15	POLR2A	chr4:76911832-76912278	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr4:76911820-76912366	SK-N-SH	brain:	n/a	n/a
17	MAX	chr4:76911642-76912352	K562	blood:	n/a	n/a
18	CHD2	chr4:76911966-76912332	Hela-S3	cervix:	n/a	n/a
19	YY1	chr4:76911899-76912343	GM12891	blood:	n/a	n/a
20	USF1	chr4:76911857-76912361	ECC-1	luminal epithelium:	n/a	n/a
21	USF1	chr4:76911922-76912256	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr4:76911928-76912371	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr4:76911589-76912428	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr4:76911815-76912330	HCT-116	colon:	n/a	n/a
25	TCF3	chr4:76911900-76912255	GM12878	blood:	n/a	n/a
26	YY1	chr4:76911718-76912275	K562	blood:	n/a	n/a
27	ELF1	chr4:76911870-76912313	HepG2	liver:	n/a	n/a
28	SIN3AK20	chr4:76911810-76912312	PANC-1	pancreas:	n/a	n/a
29	ZNF143	chr4:76911828-76912387	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr4:76911820-76912302	GM12891	blood:	n/a	n/a
31	SIN3A	chr4:76911136-76912341	H1-hESC	embryonic stem cell:	n/a	chr4:76911408-76911422
32	CBX3	chr4:76911932-76912476	K562	blood:	n/a	n/a
33	POLR2A	chr4:76911831-76912316	U87	brain:	n/a	n/a
34	POLR2A	chr4:76911822-76912308	ECC-1	luminal epithelium:	n/a	n/a
35	YY1	chr4:76911961-76912337	SK-N-SH_RA	brain:	n/a	n/a
36	MXI1	chr4:76910738-76912734	SK-N-SH	brain:	n/a	n/a
37	GABPA	chr4:76911540-76912496	MCF-7	breast:	n/a	n/a
38	USF2	chr4:76911701-76912323	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:76911630-76912408	SK-N-MC	brain:	n/a	n/a
40	IRF1	chr4:76911883-76912334	K562	blood:	n/a	n/a
41	MAX	chr4:76911718-76912417	HepG2	liver:	n/a	n/a
42	POLR2A	chr4:76911680-76912404	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAFK	chr4:76912043-76912336	Hela-S3	cervix:	n/a	n/a
44	USF1	chr4:76911882-76912327	A549	lung:	n/a	n/a
45	CEBPB	chr4:76912014-76912705	A549	lung:	n/a	n/a
46	SIX5	chr4:76911914-76912307	A549	lung:	n/a	n/a
47	CEBPB	chr4:76912054-76912334	K562	blood:	n/a	n/a
48	JUND	chr4:76911837-76912310	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr4:76911807-76912325	PANC-1	pancreas:	n/a	n/a
50	SIN3AK20	chr4:76911610-76912465	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:76860117..76861999-chr4:76911234..76914144,3	K562	blood:
2	chr4:76861625..76863720-chr4:76909476..76912300,3	MCF-7	breast:
3	chr4:76860117..76863006-chr4:76912184..76914144,2	K562	blood:
4	chr4:76910728..76913331-chr4:77052548..77055482,2	MCF-7	breast:
5	chr14:23563917..23564530-chr4:76911975..76912580,2	Hela-S3	cervix:
6	chr4:76910882..76913070-chr4:77069181..77071952,2	MCF-7	breast:
7	chr4:76896669..76899167-chr4:76911311..76914671,4	MCF-7	breast:

No data

Variant related genes	Relation type
SDAD1	TF binding region
ENSG00000138744	Chromatin interaction
ENSG00000198301	Chromatin interaction
ENSG00000179933	Chromatin interaction
ENSG00000138750	Chromatin interaction
ENSG00000100813	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10337	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11726292	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11735706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648437	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12648687	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651276	0.97[ASN][1000 genomes]
rs17001237	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17001273	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271527	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276885	0.84[ASN][1000 genomes]
rs2292534	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28651740	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2869460	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3733239	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796482	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796483	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4626230	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57946262	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61281201	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61487959	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66932304	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67906710	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68181445	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6840076	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6841376	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849878	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7154	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72607852	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7654068	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6838162	NUP54	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76910200-76912600	Active TSS	Right Ventricle	heart
2	chr4:76910400-76912600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr4:76910400-76912600	Active TSS	NHLF	lung
4	chr4:76910400-76912800	Active TSS	A549	lung
5	chr4:76910600-76912400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:76910600-76912600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:76910600-76912600	Active TSS	Fetal Intestine Large	intestine
8	chr4:76910800-76912400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr4:76910800-76912400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:76910800-76912400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:76910800-76912400	Active TSS	Lung	lung
12	chr4:76910800-76912600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:76910800-76912600	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr4:76910800-76912600	Active TSS	Right Atrium	heart
15	chr4:76910800-76912600	Active TSS	HSMM	muscle
16	chr4:76911000-76912400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr4:76911000-76912400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:76911000-76912400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:76911000-76912400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:76911000-76912400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:76911000-76912400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:76911000-76912400	Active TSS	Fetal Lung	lung
23	chr4:76911000-76912400	Active TSS	Fetal Muscle Leg	muscle
24	chr4:76911000-76912400	Active TSS	Gastric	stomach
25	chr4:76911000-76912400	Active TSS	Ovary	ovary
26	chr4:76911000-76912400	Active TSS	Pancreas	Pancrea
27	chr4:76911000-76912400	Active TSS	Thymus	Thymus
28	chr4:76911000-76912400	Active TSS	HSMMtube	muscle
29	chr4:76911000-76912600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr4:76911000-76912600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr4:76911000-76912600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr4:76911000-76912600	Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:76911000-76912600	Active TSS	Aorta	Aorta
34	chr4:76911000-76912600	Active TSS	Fetal Thymus	thymus
35	chr4:76911000-76912600	Active TSS	Left Ventricle	heart
36	chr4:76911000-76912600	Active TSS	K562	blood
37	chr4:76911000-76912600	Active TSS	NHDF-Ad	bronchial
38	chr4:76911000-76912600	Active TSS	NHEK	skin
39	chr4:76911000-76912800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:76911000-76912800	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr4:76911000-76912800	Active TSS	Psoas Muscle	Psoas
42	chr4:76911000-76913000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr4:76911200-76912400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:76911200-76912400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:76911200-76912400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:76911200-76912400	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr4:76911200-76912400	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr4:76911200-76912400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:76911200-76912400	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr4:76911200-76912400	Active TSS	Esophagus	oesophagus

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