Variant report

Variant	rs202052
Chromosome Location	chr6:13273836-13273837
allele	C/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	RELA	chr6:13273499-13275049	GM18951	blood:	n/a	n/a
2	ARID3A	chr6:13272972-13275162	K562	blood:	n/a	n/a
3	POLR2A	chr6:13272680-13275076	K562	blood:	n/a	n/a
4	MTA3	chr6:13272472-13275024	GM12878	blood:	n/a	n/a
5	BHLHE40	chr6:13272403-13274607	K562	blood:	n/a	chr6:13272899-13272908 chr6:13272899-13272908 chr6:13272900-13272909 chr6:13272874-13272890 chr6:13272849-13272865 chr6:13272893-13272914
6	POLR2A	chr6:13273807-13274116	GM12891	blood:	n/a	n/a
7	ZNF384	chr6:13273469-13273935	K562	blood:	n/a	n/a
8	BACH1	chr6:13273445-13273855	K562	blood:	n/a	n/a
9	MAFF	chr6:13273043-13273937	K562	blood:	n/a	n/a
10	RCOR1	chr6:13273803-13274477	GM12878	blood:	n/a	n/a
11	NFATC1	chr6:13273370-13275112	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:13273626-13274997	GM19193	blood:	n/a	n/a
13	MYC	chr6:13272686-13275149	K562	blood:	n/a	chr6:13272870-13272880
14	RELA	chr6:13273666-13274978	GM12892	blood:	n/a	n/a
15	JUN	chr6:13272018-13276804	K562	blood:	n/a	chr6:13276647-13276657
16	RCOR1	chr6:13273403-13274938	K562	blood:	n/a	n/a
17	POLR2A	chr6:13273818-13274576	GM12891	blood:	n/a	n/a
18	IRF1	chr6:13273314-13273961	K562	blood:	n/a	n/a
19	RELA	chr6:13272294-13275127	GM12891	blood:	n/a	n/a
20	POLR2A	chr6:13271984-13273855	K562	blood:	n/a	n/a
21	HEY1	chr6:13272744-13273915	K562	blood:	n/a	chr6:13272899-13272908
22	POLR2A	chr6:13273377-13273866	GM12891	blood:	n/a	n/a
23	RELA	chr6:13272249-13275025	GM19193	blood:	n/a	n/a
24	POLR2A	chr6:13272496-13275011	GM19099	blood:	n/a	n/a
25	RELA	chr6:13272415-13276072	GM10847	blood:	n/a	n/a
26	MXI1	chr6:13272866-13273916	K562	blood:	n/a	n/a
27	TBL1XR1	chr6:13272326-13274866	GM12878	blood:	n/a	n/a
28	CUX1	chr6:13273092-13274705	K562	blood:	n/a	n/a
29	EP300	chr6:13273394-13273995	K562	blood:	n/a	n/a
30	POLR2A	chr6:13272223-13276600	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:13273833-13274115	GM12891	blood:	n/a	n/a
32	ELK1	chr6:13273831-13274580	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:13272865-13274072	PBDE	blood:	n/a	n/a
34	NR2F2	chr6:13272645-13276785	K562	blood:	n/a	n/a
35	TBL1XR1	chr6:13273325-13275040	K562	blood:	n/a	n/a
36	PML	chr6:13272251-13275171	GM12878	blood:	n/a	n/a
37	NFATC1	chr6:13273751-13274691	GM12878	blood:	n/a	n/a
38	RUNX3	chr6:13272292-13274947	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:13272237-13275957	GM12892	blood:	n/a	n/a
40	POLR2A	chr6:13272526-13275090	GM18505	blood:	n/a	n/a
41	MYC	chr6:13272462-13274998	K562	blood:	n/a	chr6:13272870-13272880
42	MXI1	chr6:13272324-13275420	GM12878	blood:	n/a	n/a
43	STAT5A	chr6:13272382-13275170	GM12878	blood:	n/a	chr6:13272427-13272439
44	TEAD4	chr6:13272318-13275177	K562	blood:	n/a	n/a
45	HCFC1	chr6:13272799-13273966	K562	blood:	n/a	n/a
46	CUX1	chr6:13273504-13274910	GM12878	blood:	n/a	n/a
47	BHLHE40	chr6:13272222-13275037	GM12878	blood:	n/a	chr6:13272899-13272908 chr6:13272899-13272908 chr6:13272900-13272909 chr6:13272874-13272890 chr6:13272849-13272865 chr6:13272893-13272914
48	PML	chr6:13272714-13273955	K562	blood:	n/a	n/a
49	POLR2A	chr6:13271496-13276674	K562	blood:	n/a	n/a
50	POLR2A	chr6:13272368-13276162	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13268970..13278598-chr6:13326296..13332818,15	K562	blood:
2	chr6:13273285..13276286-chr6:13486162..13489029,4	K562	blood:
3	chr6:13273285..13276286-chr6:13486162..13489029,3	K562	blood:
4	chr6:13272896..13275816-chr6:13711430..13713666,2	K562	blood:
5	chr6:13272205..13274313-chr6:13327989..13330165,3	K562	blood:

Variant related genes	Relation type
PHACTR1	TF binding region
ENSG00000010017	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11966270	0.81[EUR][1000 genomes]
rs11968818	0.81[EUR][1000 genomes]
rs12525892	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12525906	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12527422	0.81[EUR][1000 genomes]
rs12660606	0.81[EUR][1000 genomes]
rs12665408	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1736501	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1736502	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs175729	0.81[EUR][1000 genomes]
rs17667989	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1937765	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202024	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202026	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202031	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs202033	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs202037	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs202043	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202049	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs202055	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202056	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202059	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs202061	0.81[EUR][1000 genomes]
rs202065	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs202067	0.85[AMR][1000 genomes]
rs202075	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202078	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369946	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs413167	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs417024	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs429919	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs429935	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs430216	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs434703	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs434923	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs436268	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs443150	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711948	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711949	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4711956	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4715168	0.83[EUR][1000 genomes]
rs533512	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs534449	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs555496	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs602976	0.81[EUR][1000 genomes]
rs644309	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7765972	0.81[AMR][1000 genomes];0.83[EUR][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202052	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
3	chr6:13267000-13274200	Weak transcription	Gastric	stomach
4	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
6	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:13269400-13274200	Weak transcription	Aorta	Aorta
10	chr6:13269400-13275400	Weak transcription	Right Ventricle	heart
11	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
12	chr6:13269600-13275600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:13270200-13291600	Weak transcription	HSMM	muscle
16	chr6:13270400-13282000	Weak transcription	Ovary	ovary
17	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
18	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
21	chr6:13272000-13274000	Enhancers	Brain Substantia Nigra	brain
22	chr6:13272000-13275800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr6:13272200-13274400	Enhancers	Brain Anterior Caudate	brain
24	chr6:13272200-13274400	Enhancers	Brain Cingulate Gyrus	brain
25	chr6:13272200-13275800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr6:13272200-13276200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:13272400-13274000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:13272400-13275600	Enhancers	Placenta	Placenta
29	chr6:13272400-13275600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:13272400-13276600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:13272600-13274000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr6:13272600-13274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:13272600-13275200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:13272600-13275600	Active TSS	Rectal Smooth Muscle	rectum
35	chr6:13272800-13274400	Active TSS	Primary B cells from peripheral blood	blood
36	chr6:13272800-13274400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:13272800-13274800	Enhancers	Fetal Thymus	thymus
38	chr6:13272800-13275400	Weak transcription	Spleen	Spleen
39	chr6:13273000-13274000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr6:13273000-13274000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:13273000-13274800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:13273000-13274800	Active TSS	Duodenum Mucosa	Duodenum
43	chr6:13273000-13275000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr6:13273000-13275000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr6:13273000-13275000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:13273000-13275400	Active TSS	GM12878-XiMat	blood
47	chr6:13273000-13275600	Active TSS	Adipose Nuclei	Adipose
48	chr6:13273000-13277200	Weak transcription	Lung	lung
49	chr6:13273000-13277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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