Variant report

Variant	rs622538
Chromosome Location	chr15:41133744-41133745
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
2	chr15:41120623..41123465-chr15:41132832..41134627,2	K562	blood:
3	chr15:41129410..41132304-chr15:41132946..41134611,2	K562	blood:
4	chr15:41121981..41124134-chr15:41133402..41135573,2	MCF-7	breast:
5	chr15:41118647..41120518-chr15:41133516..41135113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166143	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000166140	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11639292	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2291618	0.98[ASN][1000 genomes]
rs2412569	0.98[EUR][1000 genomes]
rs2412570	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2917953	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3759798	0.98[ASN][1000 genomes]
rs59831883	0.95[ASN][1000 genomes]
rs668708	0.86[EUR][1000 genomes]
rs668750	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs680493	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689589	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689594	0.89[EUR][1000 genomes]
rs689618	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs689733	0.84[EUR][1000 genomes]
rs689736	0.85[AFR][1000 genomes];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
rs622538	RP11-111A22.1	cis	Artery Tibial	GTEx
rs622538	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs622538	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:23 , 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	chr15:41121600-41135200	Weak transcription	Colonic Mucosa	Colon
7	chr15:41121600-41135200	Weak transcription	Gastric	stomach
8	chr15:41121600-41135200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:41121800-41135200	Weak transcription	Stomach Mucosa	stomach
10	chr15:41122800-41135000	Weak transcription	Fetal Intestine Large	intestine
11	chr15:41123200-41135600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:41123600-41135000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:41124800-41135200	Weak transcription	Pancreas	Pancrea
14	chr15:41131200-41134200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:41131200-41135400	Weak transcription	Lung	lung
16	chr15:41131200-41135600	Weak transcription	K562	blood
17	chr15:41131400-41135000	Weak transcription	HMEC	breast
18	chr15:41131400-41135200	Weak transcription	Placenta	Placenta
19	chr15:41132600-41135000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:41132600-41135000	Weak transcription	Fetal Intestine Small	intestine
21	chr15:41132600-41135200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:41133000-41134400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:41133600-41135200	Weak transcription	Fetal Kidney	kidney

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