Variant report

Variant	rs8124053
Chromosome Location	chr20:1395793-1395794
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1389651..1392477-chr20:1392965..1396440,4	K562	blood:
2	chr20:1308822..1311082-chr20:1395748..1398133,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11087052	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13063	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs1884389	0.81[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1884391	0.83[JPT][hapmap]
rs1998007	0.93[ASN][1000 genomes]
rs2144542	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2144543	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2144545	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs2207828	0.87[ASN][1000 genomes]
rs2207829	0.93[ASN][1000 genomes]
rs2207830	0.89[ASN][1000 genomes]
rs3088080	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs3171292	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs3210915	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs36018423	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4352285	0.83[CHD][hapmap];0.84[JPT][hapmap]
rs4546067	0.84[JPT][hapmap]
rs4813133	0.93[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4814229	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814231	0.93[ASN][1000 genomes]
rs4814237	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814240	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814243	0.80[ASN][1000 genomes]
rs4814244	0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs5019244	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033691	0.93[ASN][1000 genomes]
rs6033697	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033698	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033707	0.93[ASN][1000 genomes]
rs6033709	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033715	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033726	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033728	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033729	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033732	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033744	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033753	0.81[ASN][1000 genomes]
rs6033807	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs6042066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042071	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042072	0.93[ASN][1000 genomes]
rs6042074	0.93[ASN][1000 genomes]
rs6042088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042091	0.93[ASN][1000 genomes]
rs6042117	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042118	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042131	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042160	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042170	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042172	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042175	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042207	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042208	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042244	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs6042270	0.89[JPT][hapmap]
rs6042292	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs6042354	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs6074593	0.93[ASN][1000 genomes]
rs6074623	0.85[ASN][1000 genomes]
rs6079009	0.93[ASN][1000 genomes]
rs6079010	0.93[ASN][1000 genomes]
rs6079012	0.93[ASN][1000 genomes]
rs6079013	0.93[ASN][1000 genomes]
rs6079015	0.93[ASN][1000 genomes]
rs6079133	0.88[JPT][hapmap]
rs6105079	0.93[ASN][1000 genomes]
rs6105081	0.93[ASN][1000 genomes]
rs6105102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6105110	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6105165	0.89[JPT][hapmap]
rs6109825	0.93[ASN][1000 genomes]
rs6109893	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109894	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6109912	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6131468	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134916	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6514382	0.93[ASN][1000 genomes]
rs6514383	0.93[ASN][1000 genomes]
rs6891	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs750424	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs910619	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs910620	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs926977	0.81[ASN][1000 genomes]
rs932524	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs9575	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1817885	chr20:1386940-1400227	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1818242	chr20:1389773-1400227	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1843659	chr20:1389773-1400227	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1843922	chr20:1389773-1400227	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1820441	chr20:1389863-1397898	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8124053	NSFL1C	cis	cerebellum	SCAN
rs8124053	CENPB	cis	cerebellum	SCAN
rs8124053	DEFB125	cis	cerebellum	SCAN
rs8124053	NSFL1C	cis	Brain Pons	GTEx
rs8124053	NSFL1C	cis	Temporal Cortex	GTEx
rs8124053	NSFL1C	cis	Frontal Cortex	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1383800-1396000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr20:1384400-1396000	Weak transcription	HMEC	breast
3	chr20:1389000-1396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr20:1389200-1396400	Weak transcription	Placenta	Placenta
5	chr20:1390600-1396600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:1395000-1396200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:1395600-1395800	Flanking Active TSS	A549	lung
8	chr20:1395600-1397200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr20:1395600-1398000	Weak transcription	Spleen	Spleen
10	chr20:1395600-1399600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:1395600-1399800	Enhancers	NHLF	lung
12	chr20:1395600-1400000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:1395600-1400000	Enhancers	NHDF-Ad	bronchial
14	chr20:1395600-1400200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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