Variant report

Variant	rs11639292
Chromosome Location	chr15:41129528-41129529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:41127204..41130977-chr15:41135554..41137561,3	K562	blood:
2	chr15:41124557..41126932-chr15:41129438..41132345,2	K562	blood:
3	chr15:41127361..41129926-chr15:41131042..41133527,3	K562	blood:
4	chr15:41129410..41132304-chr15:41132946..41134611,2	K562	blood:
5	chr15:41129275..41132805-chr15:41134409..41137816,5	MCF-7	breast:
6	chr15:41116376..41117898-chr15:41128674..41130179,2	MCF-7	breast:
7	chr15:41127340..41129810-chr15:41135793..41138120,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPINT1-1	chr15:41128776-41129560	NONHSAT041886

No data

Variant related genes	Relation type
ENSG00000261183	Chromatin interaction
ENSG00000166145	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2412569	0.98[EUR][1000 genomes]
rs2412570	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2917953	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs622538	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs668708	0.87[EUR][1000 genomes]
rs668750	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs680493	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689589	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689594	0.89[EUR][1000 genomes]
rs689618	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs689733	0.84[EUR][1000 genomes]
rs689736	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690435	0.88[EUR][1000 genomes]
rs690572	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs690660	0.98[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11639292	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11639292	C15orf57	cis	Artery Tibial	GTEx
rs11639292	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41107200-41135200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:41107600-41135200	Weak transcription	Esophagus	oesophagus
3	chr15:41108200-41135600	Weak transcription	Spleen	Spleen
4	chr15:41112000-41135800	Weak transcription	Right Atrium	heart
5	chr15:41120800-41135600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:41121600-41129800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:41121600-41135200	Weak transcription	Colonic Mucosa	Colon
8	chr15:41121600-41135200	Weak transcription	Gastric	stomach
9	chr15:41121600-41135200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:41121800-41135200	Weak transcription	Stomach Mucosa	stomach
11	chr15:41122800-41135000	Weak transcription	Fetal Intestine Large	intestine
12	chr15:41123200-41135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:41123600-41135000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:41124800-41135200	Weak transcription	Pancreas	Pancrea
15	chr15:41127400-41131000	Weak transcription	Placenta	Placenta
16	chr15:41128000-41130600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:41128400-41130600	Weak transcription	HMEC	breast
18	chr15:41128400-41130800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:41128600-41130400	Weak transcription	Fetal Intestine Small	intestine
20	chr15:41128600-41130800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:41129000-41129800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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