Variant report

Variant	rs202048
Chromosome Location	chr6:13274501-13274502
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:168)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:168 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr6:13274191-13274551	K562	blood:	n/a	n/a
2	RELA	chr6:13273499-13275049	GM18951	blood:	n/a	n/a
3	EP300	chr6:13274054-13274905	GM12878	blood:	n/a	n/a
4	MAX	chr6:13274105-13274563	K562	blood:	n/a	n/a
5	CHD2	chr6:13273881-13275062	GM12878	blood:	n/a	n/a
6	BRCA1	chr6:13274214-13274530	GM12878	blood:	n/a	n/a
7	ARID3A	chr6:13272972-13275162	K562	blood:	n/a	n/a
8	ZNF384	chr6:13274196-13274703	K562	blood:	n/a	n/a
9	ZMIZ1	chr6:13274132-13275106	K562	blood:	n/a	n/a
10	POLR2A	chr6:13272680-13275076	K562	blood:	n/a	n/a
11	ELF1	chr6:13274101-13274598	GM12878	blood:	n/a	n/a
12	MTA3	chr6:13272472-13275024	GM12878	blood:	n/a	n/a
13	NFIC	chr6:13273906-13274718	GM12878	blood:	n/a	n/a
14	NR2F2	chr6:13274097-13275072	K562	blood:	n/a	n/a
15	POLR2A	chr6:13273892-13275054	K562	blood:	n/a	n/a
16	PML	chr6:13274122-13275165	K562	blood:	n/a	n/a
17	POLR2A	chr6:13273988-13274864	GM12891	blood:	n/a	n/a
18	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
19	POLR2A	chr6:13274116-13274614	HL-60	blood:	n/a	n/a
20	POLR2A	chr6:13274111-13274536	GM12878	blood:	n/a	n/a
21	MAX	chr6:13274089-13274526	K562	blood:	n/a	n/a
22	CREB1	chr6:13274045-13274646	GM12878	blood:	n/a	n/a
23	EP300	chr6:13273885-13274762	GM12878	blood:	n/a	n/a
24	EGR1	chr6:13274124-13274996	K562	blood:	n/a	chr6:13274343-13274357
25	TRIM28	chr6:13274120-13275112	K562	blood:	n/a	n/a
26	NFATC1	chr6:13273370-13275112	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:13273626-13274997	GM19193	blood:	n/a	n/a
28	MYC	chr6:13272686-13275149	K562	blood:	n/a	chr6:13272870-13272880
29	POLR2A	chr6:13274029-13274637	K562	blood:	n/a	n/a
30	REST	chr6:13274230-13274509	K562	blood:	n/a	n/a
31	POLR2A	chr6:13274119-13275037	K562	blood:	n/a	n/a
32	RELA	chr6:13273919-13275120	GM12878	blood:	n/a	n/a
33	POU2F2	chr6:13274074-13274573	GM12891	blood:	n/a	n/a
34	RELA	chr6:13273666-13274978	GM12892	blood:	n/a	n/a
35	JUN	chr6:13272018-13276804	K562	blood:	n/a	chr6:13276647-13276657
36	RCOR1	chr6:13273403-13274938	K562	blood:	n/a	n/a
37	ZNF143	chr6:13274135-13274520	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:13273818-13274576	GM12891	blood:	n/a	n/a
39	RELA	chr6:13272294-13275127	GM12891	blood:	n/a	n/a
40	UBTF	chr6:13274153-13275060	K562	blood:	n/a	n/a
41	TAL1	chr6:13274188-13274964	K562	blood:	n/a	n/a
42	REST	chr6:13274127-13275030	K562	blood:	n/a	n/a
43	RELA	chr6:13272249-13275025	GM19193	blood:	n/a	n/a
44	EGR1	chr6:13274143-13274539	GM12878	blood:	n/a	chr6:13274343-13274357
45	POLR2A	chr6:13272496-13275011	GM19099	blood:	n/a	n/a
46	RELA	chr6:13272415-13276072	GM10847	blood:	n/a	n/a
47	CEBPB	chr6:13273980-13274741	GM12878	blood:	n/a	n/a
48	POU2F2	chr6:13273988-13274540	GM12878	blood:	n/a	n/a
49	SPI1	chr6:13274113-13274581	GM12891	blood:	n/a	n/a
50	CEBPB	chr6:13274115-13274610	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

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	chr6:13274197..13275936-chr6:13573987..13576342,2	K562	blood:
5	chr6:13274000..13275754-chr6:13276034..13278687,2	MCF-7	breast:
6	chr6:13272896..13275816-chr6:13711430..13713666,2	K562	blood:
7	chr6:13246618..13250195-chr6:13274363..13276198,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215022	TF binding region
PHACTR1	TF binding region
ENSG00000010017	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000112137	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11759028	0.84[ASN][1000 genomes]
rs1223393	0.86[EUR][1000 genomes]
rs12697949	0.81[ASN][1000 genomes]
rs1550526	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs182148	0.89[EUR][1000 genomes]
rs202028	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202030	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202034	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202038	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202040	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202045	0.82[ASN][1000 genomes]
rs202046	0.82[ASN][1000 genomes]
rs202051	0.80[ASN][1000 genomes]
rs202064	0.84[EUR][1000 genomes]
rs202068	0.89[EUR][1000 genomes]
rs202069	0.89[EUR][1000 genomes]
rs35952102	0.87[ASN][1000 genomes]
rs3800481	0.87[ASN][1000 genomes]
rs3800482	0.87[ASN][1000 genomes]
rs3800483	0.87[ASN][1000 genomes]
rs3800484	0.87[ASN][1000 genomes]
rs3800485	0.87[ASN][1000 genomes]
rs3800486	0.87[ASN][1000 genomes]
rs3823442	0.86[ASN][1000 genomes]
rs3823443	0.86[ASN][1000 genomes]
rs453695	0.84[EUR][1000 genomes]
rs454563	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4602719	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs515111	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs536208	0.81[EUR][1000 genomes]
rs6914796	0.85[ASN][1000 genomes]
rs7742398	0.87[ASN][1000 genomes]
rs8541	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9473929	0.87[ASN][1000 genomes]
rs9473930	0.87[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	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

No data

Chromatin state (count:83 , 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	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
5	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:13269400-13275400	Weak transcription	Right Ventricle	heart
9	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
10	chr6:13269600-13275600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:13270200-13291600	Weak transcription	HSMM	muscle
14	chr6:13270400-13282000	Weak transcription	Ovary	ovary
15	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
16	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
19	chr6:13272000-13275800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr6:13272200-13275800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr6:13272200-13276200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:13272400-13275600	Enhancers	Placenta	Placenta
23	chr6:13272400-13275600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:13272400-13276600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:13272600-13274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr6:13272600-13275200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:13272600-13275600	Active TSS	Rectal Smooth Muscle	rectum
28	chr6:13272800-13274800	Enhancers	Fetal Thymus	thymus
29	chr6:13272800-13275400	Weak transcription	Spleen	Spleen
30	chr6:13273000-13274800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:13273000-13274800	Active TSS	Duodenum Mucosa	Duodenum
32	chr6:13273000-13275000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr6:13273000-13275000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:13273000-13275000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:13273000-13275400	Active TSS	GM12878-XiMat	blood
36	chr6:13273000-13275600	Active TSS	Adipose Nuclei	Adipose
37	chr6:13273000-13277200	Weak transcription	Lung	lung
38	chr6:13273000-13277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:13273200-13274600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:13273200-13277200	Weak transcription	Left Ventricle	heart
42	chr6:13273400-13274600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr6:13273400-13274800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:13273400-13274800	Active TSS	Thymus	Thymus
45	chr6:13273400-13275000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:13273400-13275800	Weak transcription	Brain Germinal Matrix	brain
47	chr6:13273400-13286800	Weak transcription	Liver	Liver
48	chr6:13273600-13274600	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr6:13273600-13274600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:13273600-13275000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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