Variant report

Variant	rs55810735
Chromosome Location	chr3:56718230-56718231
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	TCF7L2	chr3:56717403-56718599	HEK293	kidney:	n/a	n/a
2	POLR2A	chr3:56718118-56718541	MCF10A-Er-Src	breast:	n/a	n/a
3	SETDB1	chr3:56717252-56718475	U2OS	brain:	n/a	n/a
4	ZNF263	chr3:56716001-56718555	HEK293-T-REx	kidney:	n/a	chr3:56717929-56717938 chr3:56717242-56717251
5	KAP1	chr3:56717363-56718703	HEK293	kidney:	n/a	chr3:56717806-56717814
6	KAP1	chr3:56717375-56718687	U2OS	brain:	n/a	chr3:56717806-56717814

No.	Distal block	Cell Line	Cell type
1	chr3:56589231..56591997-chr3:56715959..56718849,3	K562	blood:
2	chr3:56702147..56705420-chr3:56716741..56719178,3	MCF-7	breast:
3	chr3:56589586..56592975-chr3:56714350..56719200,6	K562	blood:
4	chr3:56715514..56718317-chr3:56833414..56836251,4	MCF-7	breast:

Variant related genes	Relation type
FAM208A	TF binding region
ENSG00000163946	Chromatin interaction
ENSG00000180376	Chromatin interaction
ENSG00000163947	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10865997	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12486047	0.84[EUR][1000 genomes]
rs1565378	0.82[AMR][1000 genomes]
rs282524	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282526	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282537	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732513	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681736	0.82[AMR][1000 genomes]
rs4682001	0.82[AMR][1000 genomes]
rs4682002	0.82[AMR][1000 genomes]
rs4974218	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4974222	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66873962	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6769055	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7620896	0.82[AMR][1000 genomes]
rs7639731	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7640995	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs873840	0.82[AMR][1000 genomes]
rs955248	0.86[EUR][1000 genomes]
rs9834064	0.80[EUR][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	esv3327056	chr3:56715937-56718485	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55810735	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56717400-56718400	ZNF genes & repeats	HSMM	muscle
2	chr3:56717400-56718600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:56717600-56718400	Enhancers	HepG2	liver
4	chr3:56717600-56718600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:56717600-56718800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:56717600-56725200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:56717600-56725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:56717800-56718600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:56717800-56718600	ZNF genes & repeats	GM12878-XiMat	blood
10	chr3:56717800-56718800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr3:56717800-56719400	Weak transcription	Fetal Kidney	kidney
12	chr3:56717800-56720200	Weak transcription	Fetal Lung	lung
13	chr3:56717800-56720800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:56717800-56722000	Weak transcription	Primary B cells from cord blood	blood
15	chr3:56717800-56725200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:56717800-56725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:56717800-56726800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:56718000-56719000	Strong transcription	Fetal Thymus	thymus
19	chr3:56718000-56719400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:56718000-56719600	Weak transcription	Fetal Stomach	stomach
21	chr3:56718000-56719800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:56718000-56722000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:56718000-56722200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:56718000-56723400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:56718000-56725200	Weak transcription	Dnd41	blood
26	chr3:56718000-56725200	Weak transcription	HMEC	breast
27	chr3:56718000-56727000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:56718000-56727400	Weak transcription	HSMMtube	muscle
29	chr3:56718200-56718400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:56718200-56718400	ZNF genes & repeats	NH-A	brain
31	chr3:56718200-56719000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr3:56718200-56722400	Weak transcription	NHEK	skin
33	chr3:56718200-56725000	Weak transcription	Placenta	Placenta

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