Variant report

Variant	rs690572
Chromosome Location	chr15:41135406-41135407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41135393-41136741	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41131767..41134219-chr15:41134403..41136032,2	MCF-7	breast:
2	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
3	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
4	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
5	chr15:41121981..41124134-chr15:41133402..41135573,2	MCF-7	breast:
6	chr15:41050847..41052798-chr15:41135268..41136987,2	K562	blood:
7	chr15:41099271..41102222-chr15:41135281..41137187,2	K562	blood:
8	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
9	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
10	chr15:41129275..41132805-chr15:41134409..41137816,5	MCF-7	breast:
11	chr15:40985736..40987452-chr15:41134754..41137017,2	MCF-7	breast:
12	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261183	TF binding region
SPINT1	TF binding region
ENSG00000166140	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000271236	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11639292	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2412569	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412570	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917953	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622538	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6492962	1.00[JPT][hapmap]
rs668708	0.87[EUR][1000 genomes]
rs668750	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680493	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689589	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689594	1.00[CEU][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs689618	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689733	0.86[EUR][1000 genomes]
rs689736	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690435	0.89[EUR][1000 genomes]
rs690660	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs690572	MRPL42P5	cis	multi-tissue	Pritchard
rs690572	RP11-111A22.1	cis	Artery Tibial	GTEx
rs690572	SPINT1	cis	multi-tissue	Pritchard
rs690572	C15orf57	cis	Artery Tibial	GTEx
rs690572	ZFYVE19	cis	cerebellum	SCAN
rs690572	ZFYVE19	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41108200-41135600	Weak transcription	Spleen	Spleen
2	chr15:41112000-41135800	Weak transcription	Right Atrium	heart
3	chr15:41120800-41135600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:41123200-41135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:41131200-41135600	Weak transcription	K562	blood
6	chr15:41135000-41135800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr15:41135000-41135800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:41135000-41135800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr15:41135000-41135800	Flanking Active TSS	NHEK	skin
10	chr15:41135200-41135600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr15:41135200-41135600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr15:41135200-41135600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
13	chr15:41135200-41135600	Active TSS	Colonic Mucosa	Colon
14	chr15:41135200-41135600	Bivalent Enhancer	Fetal Thymus	thymus
15	chr15:41135200-41135600	Enhancers	Pancreas	Pancrea
16	chr15:41135200-41135800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:41135200-41135800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:41135200-41135800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
19	chr15:41135200-41135800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr15:41135200-41136000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:41135200-41136000	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr15:41135200-41136000	Flanking Active TSS	Stomach Mucosa	stomach
23	chr15:41135200-41136000	Flanking Active TSS	HMEC	breast
24	chr15:41135200-41137800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr15:41135200-41138800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr15:41135200-41139000	Active TSS	Fetal Kidney	kidney
27	chr15:41135400-41135600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:41135400-41135600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
29	chr15:41135400-41135600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
30	chr15:41135400-41135600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:41135400-41135600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:41135400-41135600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:41135400-41135600	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr15:41135400-41135600	Weak transcription	Gastric	stomach
35	chr15:41135400-41135600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:41135400-41135600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
37	chr15:41135400-41135800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr15:41135400-41135800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
39	chr15:41135400-41135800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:41135400-41135800	Enhancers	Primary B cells from cord blood	blood
41	chr15:41135400-41135800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:41135400-41135800	Flanking Active TSS	Esophagus	oesophagus
43	chr15:41135400-41135800	Bivalent Enhancer	Fetal Lung	lung
44	chr15:41135400-41135800	Flanking Active TSS	Lung	lung
45	chr15:41135400-41135800	Flanking Bivalent TSS/Enh	HepG2	liver
46	chr15:41135400-41136000	Flanking Active TSS	Placenta	Placenta
47	chr15:41135400-41137000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr15:41135400-41137000	Active TSS	Duodenum Mucosa	Duodenum
49	chr15:41135400-41137400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:41135400-41137600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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