Variant report

Variant	rs3828655
Chromosome Location	chr5:108084178-108084179
allele	A/G
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	SIN3AK20	chr5:108084107-108084495	HepG2	liver:	n/a	n/a
2	EP300	chr5:108084037-108084975	A549	lung:	n/a	chr5:108084709-108084718
3	GTF2B	chr5:108083914-108084566	K562	blood:	n/a	n/a
4	CHD1	chr5:108083239-108084998	GM12878	blood:	n/a	chr5:108084746-108084756
5	TEAD4	chr5:108083877-108084378	H1-hESC	embryonic stem cell:	n/a	n/a
6	SP1	chr5:108083807-108085091	H1-hESC	embryonic stem cell:	n/a	chr5:108084075-108084087 chr5:108084488-108084499 chr5:108084468-108084477 chr5:108084990-108085002 chr5:108084747-108084756 chr5:108084077-108084086 chr5:108084467-108084481 chr5:108085023-108085035 chr5:108084075-108084087 chr5:108084972-108084981 chr5:108084859-108084873 chr5:108084990-108085002 chr5:108084431-108084442 chr5:108084467-108084476 chr5:108084743-108084757 chr5:108084746-108084758 chr5:108085066-108085075 chr5:108084076-108084090 chr5:108084527-108084548 chr5:108084466-108084477 chr5:108085065-108085077 chr5:108084746-108084758 chr5:108084750-108084764 chr5:108085023-108085035 chr5:108085065-108085077 chr5:108084991-108085001
7	MYC	chr5:108083367-108085620	K562	blood:	n/a	chr5:108084490-108084500 chr5:108084991-108085001 chr5:108085022-108085032
8	POLR2A	chr5:108083718-108085342	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:108083290-108084910	GM12892	blood:	n/a	n/a
10	POLR2A	chr5:108083378-108085379	GM15510	blood:	n/a	n/a
11	RCOR1	chr5:108083265-108085555	K562	blood:	n/a	n/a
12	STAT5A	chr5:108084059-108084519	GM12878	blood:	n/a	n/a
13	ZMIZ1	chr5:108083489-108084972	K562	blood:	n/a	n/a
14	RELA	chr5:108083388-108085613	GM15510	blood:	n/a	n/a
15	FOXM1	chr5:108083940-108085069	ECC-1	luminal epithelium:	n/a	n/a
16	UBTF	chr5:108083904-108084608	K562	blood:	n/a	n/a
17	RUNX3	chr5:108083980-108085660	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:108084043-108085176	GM10847	blood:	n/a	n/a
19	CTBP2	chr5:108083884-108085511	H1-hESC	embryonic stem cell:	n/a	n/a
20	RELA	chr5:108083363-108084991	GM18951	blood:	n/a	n/a
21	PML	chr5:108083201-108085404	GM12878	blood:	n/a	n/a
22	NFIC	chr5:108084152-108084509	HepG2	liver:	n/a	n/a
23	TAF1	chr5:108084133-108084516	GM12892	blood:	n/a	n/a
24	NFYB	chr5:108084122-108084951	GM12878	blood:	n/a	chr5:108084534-108084549 chr5:108084611-108084626 chr5:108084611-108084626 chr5:108084534-108084549 chr5:108084450-108084465 chr5:108084537-108084547 chr5:108084535-108084549 chr5:108084538-108084550 chr5:108084536-108084551
25	RAD21	chr5:108083421-108085435	IMR90	lung:	n/a	chr5:108084040-108084052
26	CREB1	chr5:108084167-108085247	A549	lung:	n/a	n/a
27	POLR2A	chr5:108084158-108084815	HepG2	liver:	n/a	n/a
28	TEAD4	chr5:108083862-108084344	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr5:108083270-108085108	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr5:108083834-108085148	ECC-1	luminal epithelium:	n/a	n/a
31	ZBTB7A	chr5:108084122-108084585	K562	blood:	n/a	chr5:108084407-108084418
32	POLR2A	chr5:108083885-108085434	Gliobla	brain:	n/a	n/a
33	TCF12	chr5:108084125-108084846	GM12878	blood:	n/a	n/a
34	SMC3	chr5:108083341-108085634	Hela-S3	cervix:	n/a	chr5:108084470-108084480
35	TAF1	chr5:108084155-108084556	SK-N-SH	brain:	n/a	n/a
36	IRF1	chr5:108083253-108084864	K562	blood:	n/a	chr5:108084615-108084624 chr5:108084538-108084547 chr5:108084464-108084478
37	E2F6	chr5:108083953-108085428	K562	blood:	n/a	chr5:108085038-108085045 chr5:108084704-108084711 chr5:108084920-108084932 chr5:108085038-108085045 chr5:108084703-108084712 chr5:108084704-108084711 chr5:108084699-108084714 chr5:108084704-108084711 chr5:108085038-108085045 chr5:108084468-108084477 chr5:108084508-108084518
38	POLR2A	chr5:108083285-108085007	GM12878	blood:	n/a	n/a
39	TAF1	chr5:108084085-108084695	MCF-7	breast:	n/a	n/a
40	POLR2A	chr5:108083265-108085368	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr5:108083449-108085311	HEK293	kidney:	n/a	n/a
42	MAX	chr5:108083794-108085178	ECC-1	luminal epithelium:	n/a	chr5:108084490-108084500 chr5:108084991-108085001 chr5:108085022-108085032
43	MYC	chr5:108084039-108085088	MCF10A-Er-Src	breast:	n/a	chr5:108084490-108084500 chr5:108084991-108085001 chr5:108085022-108085032
44	POLR2A	chr5:108083979-108085516	HCT-116	colon:	n/a	n/a
45	POLR2A	chr5:108084005-108085553	H1-neurons	neurons:	n/a	n/a
46	TAF7	chr5:108083876-108084586	H1-hESC	embryonic stem cell:	n/a	n/a
47	EGR1	chr5:108083960-108085202	K562	blood:	n/a	chr5:108085019-108085032 chr5:108085018-108085033 chr5:108084783-108084793 chr5:108084078-108084091 chr5:108084078-108084091 chr5:108084078-108084088 chr5:108084072-108084085 chr5:108085019-108085032 chr5:108085015-108085037
48	JUND	chr5:108083850-108085285	H1-hESC	embryonic stem cell:	n/a	n/a
49	PBX3	chr5:108083998-108084963	SK-N-SH	brain:	n/a	chr5:108084537-108084546 chr5:108084422-108084442 chr5:108084453-108084462
50	UBTF	chr5:108083254-108085489	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:6875257..6876142-chr5:108083565..108084530,2	Hela-S3	cervix:
2	chr5:108060235..108074407-chr5:108078172..108087811,48	K562	blood:
3	chr5:108084102..108084832-chr5:134240296..134241074,2	Hela-S3	cervix:
4	chr11:65190155..65191154-chr5:108083330..108084319,2	Hela-S3	cervix:
5	chr16:84150098..84151007-chr5:108083828..108084368,2	Hela-S3	cervix:
6	chr5:107717757..107719316-chr5:108082854..108085189,2	MCF-7	breast:
7	chr15:90455934..90456571-chr5:108083892..108084832,2	Hela-S3	cervix:
8	chr16:46722901..46723856-chr5:108083974..108084613,2	Hela-S3	cervix:
9	chr5:108062273..108066431-chr5:108081834..108086243,5	MCF-7	breast:
10	chr5:108059312..108068052-chr5:108079113..108087366,42	K562	blood:
11	chr1:144533973..144534585-chr5:108083900..108084758,2	HCT-116	colon:
12	chr1:65468086..65468772-chr5:108083910..108084419,2	Hela-S3	cervix:
13	chr5:108082623..108084401-chr5:108745170..108746987,2	MCF-7	breast:
14	chr5:108083905..108084789-chr6:26045639..26046332,2	NB4	blood:
15	chr17:18761315..18761931-chr5:108083524..108084331,2	Hela-S3	cervix:
16	chr5:108062575..108065883-chr5:108081229..108085721,5	MCF-7	breast:
17	chr5:108082558..108084199-chr5:109024303..109026967,2	K562	blood:

Variant related genes	Relation type
FER	TF binding region
ENSG00000112893	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000198961	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000226891	Chromatin interaction
ENSG00000272523	Chromatin interaction
ENSG00000159335	Chromatin interaction
ENSG00000141127	Chromatin interaction
ENSG00000132570	Chromatin interaction
ENSG00000250021	Chromatin interaction
ENSG00000069329	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000145743	Chromatin interaction
ENSG00000260018	Chromatin interaction
ENSG00000242498	Chromatin interaction
ENSG00000140943	Chromatin interaction
ENSG00000196532	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10039132	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10066173	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10214241	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11741855	0.83[ASN][1000 genomes]
rs11748534	0.83[ASN][1000 genomes]
rs1423456	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3805600	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3805601	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62361298	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62361300	0.86[ASN][1000 genomes]
rs6869591	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6870408	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7711892	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108082600-108084800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:108082600-108085200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:108082600-108085400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:108082600-108085800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:108082600-108085800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:108082600-108085800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:108082600-108086000	Active TSS	GM12878-XiMat	blood
8	chr5:108082600-108086200	Active TSS	Right Atrium	heart
9	chr5:108082600-108087000	Active TSS	Stomach Smooth Muscle	stomach
10	chr5:108082800-108084200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:108082800-108084400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:108082800-108085400	Active TSS	Brain Anterior Caudate	brain
13	chr5:108082800-108085400	Active TSS	Osteobl	bone
14	chr5:108082800-108085600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr5:108082800-108085600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr5:108082800-108085600	Active TSS	Ovary	ovary
17	chr5:108082800-108085600	Active TSS	Right Ventricle	heart
18	chr5:108082800-108085800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr5:108082800-108085800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:108082800-108085800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:108082800-108086000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:108082800-108086200	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr5:108082800-108086200	Active TSS	NHLF	lung
24	chr5:108082800-108086400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:108082800-108086400	Active TSS	NHDF-Ad	bronchial
26	chr5:108083000-108084200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:108083000-108085200	Active TSS	Fetal Lung	lung
28	chr5:108083000-108085400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:108083000-108085400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr5:108083000-108085400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:108083000-108085400	Active TSS	NH-A	brain
32	chr5:108083000-108085600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr5:108083000-108085600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:108083000-108085800	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr5:108083000-108085800	Active TSS	Colon Smooth Muscle	Colon
36	chr5:108083000-108085800	Active TSS	Fetal Intestine Large	intestine
37	chr5:108083000-108085800	Active TSS	Psoas Muscle	Psoas
38	chr5:108083000-108085800	Active TSS	HSMMtube	muscle
39	chr5:108083000-108086000	Active TSS	NHEK	skin
40	chr5:108083200-108084400	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr5:108083200-108084400	Active TSS	Fetal Heart	heart
42	chr5:108083200-108084800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:108083200-108085400	Active TSS	Brain Angular Gyrus	brain
44	chr5:108083200-108085400	Active TSS	Fetal Kidney	kidney
45	chr5:108083200-108085400	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr5:108083200-108085400	Active TSS	K562	blood
47	chr5:108083200-108085600	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr5:108083200-108085600	Active TSS	Fetal Stomach	stomach
49	chr5:108083200-108085800	Active TSS	Fetal Intestine Small	intestine
50	chr5:108083200-108085800	Active TSS	Fetal Muscle Leg	muscle

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