Variant report

Variant	rs61553368
Chromosome Location	chr19:39543253-39543254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39542918-39543374	MCF-7	breast:	n/a	n/a
2	RAD21	chr19:39542903-39543376	A549	lung:	n/a	n/a
3	CTCF	chr19:39542907-39543280	K562	blood:	n/a	n/a
4	CTCF	chr19:39542826-39543292	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:39542846-39543578	HCT-116	colon:	n/a	n/a
6	CTCF	chr19:39542882-39543279	IMR90	lung:	n/a	n/a
7	RAD21	chr19:39542930-39543277	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF3	chr19:39542833-39543390	A549	lung:	n/a	n/a
9	RAD21	chr19:39542904-39543281	IMR90	lung:	n/a	n/a
10	CTCF	chr19:39542828-39543381	A549	lung:	n/a	n/a
11	RAD21	chr19:39542917-39543264	GM12878	blood:	n/a	n/a
12	RAD21	chr19:39542880-39543419	MCF-7	breast:	n/a	n/a
13	CTCF	chr19:39542878-39543282	GM12878	blood:	n/a	n/a
14	CTCF	chr19:39542913-39543303	A549	lung:	n/a	n/a
15	CTCF	chr19:39542909-39543326	MCF-7	breast:	n/a	n/a
16	SMC3	chr19:39542732-39543450	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr19:39542891-39543285	Hela-S3	cervix:	n/a	n/a
18	BCL3	chr19:39542804-39543617	A549	lung:	n/a	n/a
19	TCF12	chr19:39542690-39543825	A549	lung:	n/a	n/a
20	RAD21	chr19:39542868-39543529	A549	lung:	n/a	n/a
21	GTF2F1	chr19:39542941-39543277	Hela-S3	cervix:	n/a	n/a
22	RAD21	chr19:39542960-39543350	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr19:39542938-39543263	A549	lung:	n/a	n/a
24	CTCF	chr19:39543140-39543290	HCM	heart:	n/a	n/a
25	RAD21	chr19:39542895-39543474	ECC-1	luminal epithelium:	n/a	n/a
26	CTCF	chr19:39542689-39543896	A549	lung:	n/a	n/a
27	CTCF	chr19:39542916-39543271	GM19240	blood:	n/a	n/a
28	ZNF143	chr19:39542895-39543253	GM12878	blood:	n/a	n/a
29	GABPA	chr19:39542963-39543260	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr19:39542906-39543392	K562	blood:	n/a	n/a
31	RAD21	chr19:39542906-39543315	HepG2	liver:	n/a	n/a
32	RAD21	chr19:39542850-39543570	HCT-116	colon:	n/a	n/a
33	CTCF	chr19:39542690-39543471	SK-N-SH	brain:	n/a	n/a
34	MAX	chr19:39542895-39543262	NB4	blood:	n/a	chr19:39543079-39543089
35	MAX	chr19:39542905-39543274	MCF-7	breast:	n/a	chr19:39543079-39543089
36	CTCF	chr19:39542912-39543381	GM19238	blood:	n/a	n/a
37	RAD21	chr19:39542902-39543256	HepG2	liver:	n/a	n/a
38	SMC3	chr19:39542910-39543270	K562	blood:	n/a	n/a
39	RAD21	chr19:39542890-39543482	A549	lung:	n/a	n/a
40	RAD21	chr19:39542876-39543396	MCF-7	breast:	n/a	n/a
41	RAD21	chr19:39542834-39543287	SK-N-SH_RA	brain:	n/a	n/a
42	RAD21	chr19:39542898-39543290	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMC3	chr19:39542876-39543311	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr19:39542734-39543488	SK-N-SH	brain:	n/a	n/a
45	RAD21	chr19:39542850-39543572	HCT-116	colon:	n/a	n/a
46	CTCF	chr19:39542883-39543273	K562	blood:	n/a	n/a
47	ATF3	chr19:39542898-39543549	A549	lung:	n/a	n/a
48	RAD21	chr19:39542837-39543375	H1-hESC	embryonic stem cell:	n/a	n/a
49	SIN3AK20	chr19:39542985-39543399	A549	lung:	n/a	n/a
50	JUND	chr19:39542933-39543362	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39542686..39543478-chr19:39600712..39601594,2	MCF-7	breast:
2	chr19:39536592..39538414-chr19:39541757..39543284,2	MCF-7	breast:
3	chr19:39542598..39543558-chr19:39574352..39575276,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000251709	TF binding region
ENSG00000183760	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10409280	0.89[ASN][1000 genomes]
rs10411234	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10411271	0.84[ASN][1000 genomes]
rs12151099	0.83[ASN][1000 genomes]
rs12463075	0.90[ASN][1000 genomes]
rs12609401	0.93[ASN][1000 genomes]
rs12974080	0.96[ASN][1000 genomes]
rs12974708	0.89[ASN][1000 genomes]
rs12975482	0.90[ASN][1000 genomes]
rs12976100	0.89[ASN][1000 genomes]
rs12979968	0.95[ASN][1000 genomes]
rs12981133	0.93[ASN][1000 genomes]
rs12981826	0.82[AFR][1000 genomes]
rs12982067	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12983005	0.84[ASN][1000 genomes]
rs12983352	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12983682	0.83[ASN][1000 genomes]
rs12984833	0.88[ASN][1000 genomes]
rs12984836	0.88[ASN][1000 genomes]
rs13345897	0.86[ASN][1000 genomes]
rs1626050	0.93[ASN][1000 genomes]
rs1627631	0.93[ASN][1000 genomes]
rs1628376	0.93[ASN][1000 genomes]
rs1628426	0.86[ASN][1000 genomes]
rs1629253	0.93[ASN][1000 genomes]
rs1651747	0.93[ASN][1000 genomes]
rs16973058	0.90[ASN][1000 genomes]
rs1864186	0.86[ASN][1000 genomes]
rs1864188	0.86[ASN][1000 genomes]
rs1869982	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2318897	0.86[ASN][1000 genomes]
rs34240661	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34366439	0.84[ASN][1000 genomes]
rs35000840	0.88[ASN][1000 genomes]
rs35622111	0.91[ASN][1000 genomes]
rs35940388	0.85[ASN][1000 genomes]
rs4802010	0.95[ASN][1000 genomes]
rs487356	0.93[ASN][1000 genomes]
rs516901	0.93[ASN][1000 genomes]
rs523890	0.86[ASN][1000 genomes]
rs523943	0.93[ASN][1000 genomes]
rs542464	0.91[ASN][1000 genomes]
rs553330	0.93[ASN][1000 genomes]
rs554932	0.93[ASN][1000 genomes]
rs561148	0.91[ASN][1000 genomes]
rs561329	0.91[ASN][1000 genomes]
rs572764	0.93[ASN][1000 genomes]
rs57401831	0.90[ASN][1000 genomes]
rs57724551	0.86[ASN][1000 genomes]
rs582575	0.93[ASN][1000 genomes]
rs582593	0.93[ASN][1000 genomes]
rs583529	0.93[ASN][1000 genomes]
rs583995	0.93[ASN][1000 genomes]
rs584806	0.93[ASN][1000 genomes]
rs584822	0.93[ASN][1000 genomes]
rs586107	0.90[ASN][1000 genomes]
rs586176	0.93[ASN][1000 genomes]
rs59698424	0.92[ASN][1000 genomes]
rs598468	0.90[ASN][1000 genomes]
rs599230	0.93[ASN][1000 genomes]
rs602899	0.93[ASN][1000 genomes]
rs618068	0.93[ASN][1000 genomes]
rs62119464	0.86[ASN][1000 genomes]
rs62119508	0.93[ASN][1000 genomes]
rs62119510	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62121532	0.88[ASN][1000 genomes]
rs662202	0.93[ASN][1000 genomes]
rs678772	0.93[ASN][1000 genomes]
rs678848	0.93[ASN][1000 genomes]
rs679657	0.93[ASN][1000 genomes]
rs679732	0.93[ASN][1000 genomes]
rs7246076	0.89[ASN][1000 genomes]
rs930100	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2760517	chr19:39530012-39544234	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61553368	FBXO27	cis	Artery Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39541200-39546400	Weak transcription	Right Atrium	heart
2	chr19:39542200-39546600	Enhancers	Fetal Intestine Large	intestine
3	chr19:39542800-39544000	Enhancers	HepG2	liver
4	chr19:39543000-39543400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:39543000-39543400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr19:39543000-39543400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:39543000-39543400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:39543000-39543400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:39543000-39543400	Enhancers	HMEC	breast
10	chr19:39543000-39543400	Enhancers	NHEK	skin
11	chr19:39543000-39543800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:39543000-39544400	Enhancers	A549	lung
13	chr19:39543000-39544800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:39543000-39544800	Enhancers	Brain Cingulate Gyrus	brain
15	chr19:39543000-39545200	Enhancers	Brain Anterior Caudate	brain
16	chr19:39543000-39545200	Enhancers	Fetal Intestine Small	intestine
17	chr19:39543000-39545600	Enhancers	Stomach Mucosa	stomach
18	chr19:39543200-39543600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr19:39543200-39544800	Enhancers	Brain Angular Gyrus	brain
20	chr19:39543200-39544800	Enhancers	Brain Hippocampus Middle	brain
21	chr19:39543200-39544800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:39543200-39545200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:39543200-39545200	Enhancers	Brain Substantia Nigra	brain

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