Variant report

Variant	rs59566077
Chromosome Location	chr6:13212513-13212514
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	REST	chr6:13212339-13212728	K562	blood:	n/a	n/a
2	REST	chr6:13212374-13212631	MCF-7	breast:	n/a	n/a
3	REST	chr6:13212454-13212616	K562	blood:	n/a	n/a
4	REST	chr6:13212391-13212778	GM12878	blood:	n/a	n/a
5	REST	chr6:13212399-13212600	A549	lung:	n/a	n/a
6	REST	chr6:13212338-13212709	MCF-7	breast:	n/a	n/a
7	REST	chr6:13212374-13212657	Hela-S3	cervix:	n/a	n/a
8	REST	chr6:13212364-13212762	HL-60	blood:	n/a	n/a
9	REST	chr6:13212381-13212688	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr6:13212395-13212606	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr6:13212324-13212772	ECC-1	luminal epithelium:	n/a	n/a
12	REST	chr6:13212258-13212805	HL-60	blood:	n/a	n/a
13	REST	chr6:13212326-13212699	PFSK-1	brain:	n/a	n/a
14	REST	chr6:13212467-13212580	GM12878	blood:	n/a	n/a
15	REST	chr6:13212414-13212636	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RNU1-11P	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1014820	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10948550	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11751747	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11755185	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11963839	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11966270	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967582	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11968818	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11969387	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12525681	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12525892	0.90[EUR][1000 genomes]
rs12525906	0.90[EUR][1000 genomes]
rs12527422	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12527775	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528951	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528966	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12660341	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12660392	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12660606	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12661071	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665408	0.90[EUR][1000 genomes]
rs12665414	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665416	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569418	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16873855	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1736501	0.90[EUR][1000 genomes]
rs1736502	0.90[EUR][1000 genomes]
rs175729	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1937765	0.90[EUR][1000 genomes]
rs202024	0.90[EUR][1000 genomes]
rs202026	0.90[EUR][1000 genomes]
rs202055	0.90[EUR][1000 genomes]
rs202056	0.90[EUR][1000 genomes]
rs202057	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs202059	0.90[EUR][1000 genomes]
rs202061	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs202062	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs202063	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs202065	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202075	0.84[EUR][1000 genomes]
rs202076	0.82[EUR][1000 genomes]
rs2142568	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34275015	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34373947	0.91[ASN][1000 genomes]
rs364419	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs377019	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs413167	0.90[EUR][1000 genomes]
rs429919	0.90[EUR][1000 genomes]
rs429935	0.90[EUR][1000 genomes]
rs430216	0.90[EUR][1000 genomes]
rs434703	0.90[EUR][1000 genomes]
rs436268	0.90[EUR][1000 genomes]
rs443150	0.90[EUR][1000 genomes]
rs4711945	0.91[ASN][1000 genomes]
rs4711946	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711948	0.90[EUR][1000 genomes]
rs4711949	0.90[EUR][1000 genomes]
rs4711956	0.90[EUR][1000 genomes]
rs4715154	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715155	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715157	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4715158	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715159	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4715168	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715174	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715183	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715184	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs533512	0.90[EUR][1000 genomes]
rs534449	0.90[EUR][1000 genomes]
rs555496	0.90[EUR][1000 genomes]
rs58474010	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs602976	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs603394	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73355358	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73355362	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73355368	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7759256	0.83[ASN][1000 genomes]
rs7763251	0.81[ASN][1000 genomes]
rs7765972	0.85[AMR][1000 genomes];0.90[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	nsv600992	chr6:12961922-13218549	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59566077	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13178800-13217400	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:13182000-13230000	Weak transcription	Brain Angular Gyrus	brain
3	chr6:13184000-13220800	Weak transcription	Brain Germinal Matrix	brain
4	chr6:13187400-13217400	Weak transcription	Right Atrium	heart
5	chr6:13192400-13216800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:13201400-13216200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:13201600-13215600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:13202400-13213200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:13202400-13218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:13203000-13216800	Weak transcription	Adipose Nuclei	Adipose
11	chr6:13203200-13230200	Weak transcription	Fetal Stomach	stomach
12	chr6:13203600-13217400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:13205000-13214400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:13205400-13217400	Weak transcription	HSMM	muscle
15	chr6:13206400-13217400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:13206400-13229800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:13206400-13230000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:13207800-13217400	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:13208000-13217400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:13208200-13216600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:13208200-13217400	Weak transcription	Brain Anterior Caudate	brain
22	chr6:13208200-13217400	Weak transcription	Pancreas	Pancrea
23	chr6:13208200-13239800	Weak transcription	Brain Substantia Nigra	brain
24	chr6:13208400-13230200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:13208600-13217400	Weak transcription	Left Ventricle	heart
26	chr6:13209600-13215600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:13209600-13216600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:13209600-13217000	Weak transcription	HUVEC	blood vessel
29	chr6:13209800-13215400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:13211800-13213200	Strong transcription	Lung	lung
31	chr6:13211800-13213400	Strong transcription	Aorta	Aorta
32	chr6:13211800-13213400	Strong transcription	Fetal Brain Female	brain
33	chr6:13212000-13213800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:13212000-13214000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:13212000-13215400	Weak transcription	Fetal Heart	heart
36	chr6:13212200-13216800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:13212400-13212800	Weak transcription	Gastric	stomach
38	chr6:13212400-13229800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links