Variant report

Variant	rs55840738
Chromosome Location	chr15:51060127-51060128
allele	A/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:51039062..51042009-chr15:51057876..51060168,3	MCF-7	breast:
2	chr15:50644661..50647207-chr15:51058214..51061180,2	MCF-7	breast:
3	chr15:51059873..51062365-chr15:51065766..51068595,2	K562	blood:
4	chr15:51045886..51047999-chr15:51058293..51060374,2	K562	blood:
5	chr15:51056750..51061263-chr15:51087602..51092500,6	MCF-7	breast:
6	chr15:51059872..51062621-chr15:51075621..51077496,2	MCF-7	breast:
7	chr15:51054229..51056382-chr15:51058543..51060392,2	K562	blood:
8	chr15:50977319..50980700-chr15:51053372..51060901,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000241130	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000138600	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10400817	0.95[AFR][1000 genomes]
rs10400818	0.81[AFR][1000 genomes]
rs10400826	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11852701	0.95[AFR][1000 genomes]
rs12437770	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12437783	0.89[EUR][1000 genomes]
rs12437803	0.89[EUR][1000 genomes]
rs12440570	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440864	0.91[EUR][1000 genomes]
rs12442145	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12442197	0.88[EUR][1000 genomes]
rs12443283	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12592778	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12592851	0.95[AFR][1000 genomes]
rs12593998	0.95[AFR][1000 genomes]
rs12595082	0.87[EUR][1000 genomes]
rs12595118	0.95[AFR][1000 genomes]
rs12595393	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903544	0.95[AFR][1000 genomes]
rs12906508	0.95[AFR][1000 genomes]
rs12906839	0.95[AFR][1000 genomes]
rs12909429	0.95[AFR][1000 genomes]
rs12915708	0.95[AFR][1000 genomes]
rs12916038	0.95[AFR][1000 genomes]
rs12917005	0.95[AFR][1000 genomes]
rs17645935	0.88[EUR][1000 genomes]
rs17646025	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2414065	0.95[AFR][1000 genomes]
rs28470808	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28831840	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3809501	0.85[AFR][1000 genomes]
rs3896609	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55757828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56811013	0.95[AFR][1000 genomes]
rs59685680	0.91[EUR][1000 genomes]
rs60155540	0.91[EUR][1000 genomes]
rs60695341	0.92[EUR][1000 genomes]
rs7166544	0.95[AFR][1000 genomes]
rs7168211	0.81[AFR][1000 genomes]
rs7170939	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7182865	0.85[AFR][1000 genomes]
rs7183014	0.95[AFR][1000 genomes]
rs72740493	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053966	chr15:50715572-51133186	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers 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	65 gene(s)	inside rSNPs	diseases
2	nsv542383	chr15:50715572-51133186	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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	82 gene(s)	inside rSNPs	diseases
4	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1051990	chr15:50745814-51133186	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv457134	chr15:50770868-51184583	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
8	nsv471242	chr15:50770868-51184583	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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	54 gene(s)	inside rSNPs	diseases
9	nsv569396	chr15:50770868-51184583	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
10	nsv457135	chr15:50770868-51189707	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
11	nsv569397	chr15:50770868-51189707	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv1048621	chr15:50775451-51115535	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
13	nsv1047039	chr15:50782070-51187804	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv542385	chr15:50782070-51187804	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
15	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
16	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
17	nsv1036081	chr15:50818569-51097229	Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
18	nsv1055112	chr15:50822035-51133186	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	46 gene(s)	inside rSNPs	diseases
19	nsv1042372	chr15:50846461-51208891	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
20	nsv542386	chr15:50846461-51208891	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
21	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
22	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
23	nsv904212	chr15:50979738-51132170	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
24	nsv904213	chr15:51011402-51119731	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
25	nsv1044320	chr15:51016364-51074061	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
26	nsv457137	chr15:51019117-51117524	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
27	nsv569402	chr15:51019117-51117524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
28	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55840738	SPPL2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51058400-51060400	Enhancers	GM12878-XiMat	blood
2	chr15:51058400-51061000	Weak transcription	NHDF-Ad	bronchial
3	chr15:51058400-51066800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:51058600-51070200	Weak transcription	Fetal Intestine Large	intestine
5	chr15:51058800-51065800	Weak transcription	Placenta	Placenta
6	chr15:51059000-51060200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:51059000-51060200	Weak transcription	Left Ventricle	heart
8	chr15:51059000-51060200	Weak transcription	Psoas Muscle	Psoas
9	chr15:51059200-51060200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:51059200-51060200	Enhancers	A549	lung
11	chr15:51059200-51060400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr15:51059200-51061000	Enhancers	HepG2	liver
13	chr15:51059400-51061200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:51059400-51061200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:51059600-51060200	Enhancers	Hela-S3	cervix
16	chr15:51059600-51060200	Enhancers	HMEC	breast
17	chr15:51059600-51060200	Enhancers	K562	blood
18	chr15:51059600-51060400	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr15:51059800-51060600	Enhancers	Esophagus	oesophagus
20	chr15:51059800-51060800	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr15:51060000-51060200	Enhancers	Pancreas	Pancrea
22	chr15:51060000-51060400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr15:51060000-51060400	Active TSS	Right Atrium	heart
24	chr15:51060000-51060400	Active TSS	Right Ventricle	heart
25	chr15:51060000-51060600	Enhancers	Fetal Heart	heart

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