Variant report

Variant	rs59063648
Chromosome Location	chr5:112198347-112198348
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:112197782-112199402	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:112198227-112198359	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:112195946-112198491	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:112196575-112198782	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:112198229-112198384	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:112198204-112198830	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr5:112196339-112198542	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr5:112197634-112198482	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112196028..112199860-chr5:112256680..112260462,5	MCF-7	breast:
2	chr5:112041853..112044653-chr5:112197378..112199089,2	K562	blood:
3	chr5:112195906..112198557-chr5:112198644..112200582,4	MCF-7	breast:
4	chr5:112195408..112199487-chr5:112199566..112202603,4	K562	blood:
5	chr5:112196670..112199465-chr5:112228539..112231018,2	K562	blood:
6	chr5:112194408..112196977-chr5:112198175..112200544,3	MCF-7	breast:
7	chr5:112196139..112198613-chr5:112233393..112236476,4	K562	blood:
8	chr5:112152202..112156283-chr5:112195630..112198484,4	MCF-7	breast:
9	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
10	chr5:112197171..112198752-chr5:112310924..112312714,2	MCF-7	breast:
11	chr5:112196522..112198362-chr5:112219263..112221236,2	MCF-7	breast:

No data

Variant related genes	Relation type
SRP19	TF binding region
ENSG00000270067	Chromatin interaction
ENSG00000272389	Chromatin interaction
ENSG00000249947	Chromatin interaction
ENSG00000129625	Chromatin interaction
ENSG00000272869	Chromatin interaction
ENSG00000172795	Chromatin interaction
ENSG00000134982	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1109248	1.00[AMR][1000 genomes]
rs55948553	0.84[AFR][1000 genomes]
rs56875042	1.00[AMR][1000 genomes]
rs58529934	1.00[AMR][1000 genomes]
rs59028501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73789225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73789235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73789237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73789238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73789242	0.84[AFR][1000 genomes]
rs73791450	1.00[AMR][1000 genomes]
rs73791453	1.00[AMR][1000 genomes]
rs73791454	1.00[AMR][1000 genomes]
rs73791479	1.00[AMR][1000 genomes]
rs73791489	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112196400-112198400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:112196400-112198400	Active TSS	Pancreas	Pancrea
3	chr5:112196400-112198600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:112196400-112198600	Active TSS	Right Ventricle	heart
5	chr5:112196600-112198400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:112196800-112198400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:112196800-112198400	Active TSS	A549	lung
8	chr5:112196800-112198600	Active TSS	NHLF	lung
9	chr5:112197200-112198400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr5:112197400-112198400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr5:112197400-112198400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr5:112197400-112198400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr5:112197400-112199000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:112197600-112198400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:112197600-112198400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr5:112197600-112198400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:112197600-112198400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr5:112197600-112198400	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr5:112197600-112198400	Flanking Active TSS	Brain Germinal Matrix	brain
20	chr5:112197600-112198400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:112197600-112198400	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr5:112197600-112198400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr5:112197600-112198600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr5:112197600-112198600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr5:112197600-112198800	Flanking Active TSS	Liver	Liver
26	chr5:112197800-112198400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:112197800-112198400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr5:112197800-112198400	Flanking Active TSS	Colonic Mucosa	Colon
29	chr5:112197800-112198400	Flanking Active TSS	Fetal Muscle Trunk	muscle
30	chr5:112197800-112198400	Flanking Active TSS	Left Ventricle	heart
31	chr5:112197800-112198400	Flanking Active TSS	Psoas Muscle	Psoas
32	chr5:112197800-112198400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr5:112197800-112198400	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr5:112197800-112198400	Flanking Active TSS	HUVEC	blood vessel
35	chr5:112197800-112198600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:112197800-112198600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:112197800-112198600	Flanking Active TSS	Fetal Brain Female	brain
38	chr5:112197800-112198600	Flanking Active TSS	Fetal Lung	lung
39	chr5:112197800-112198600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr5:112197800-112198800	Enhancers	Primary B cells from peripheral blood	blood
41	chr5:112197800-112198800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:112197800-112200000	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr5:112197800-112211800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr5:112198000-112198400	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
45	chr5:112198000-112198400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr5:112198000-112198400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr5:112198000-112198400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr5:112198000-112198400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr5:112198000-112198400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:112198000-112198400	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links