Variant report

Variant	rs559299
Chromosome Location	chr6:145431523-145431524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:145422459..145425405-chr6:145430623..145432232,2	MCF-7	breast:
2	chr6:145430494..145433220-chr6:145468971..145470857,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1007379	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13192528	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328639	0.91[EUR][1000 genomes]
rs2761089	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788713	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2788720	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs477572	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs480110	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs499988	0.93[EUR][1000 genomes]
rs510141	0.94[EUR][1000 genomes]
rs512985	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs514258	0.95[EUR][1000 genomes]
rs515224	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs519680	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs521471	0.93[EUR][1000 genomes]
rs524563	0.81[AMR][1000 genomes]
rs526564	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs529733	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539661	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs540319	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs544904	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs561083	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs565687	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs572490	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs584911	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs605757	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607623	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs609639	0.97[EUR][1000 genomes]
rs620561	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs621529	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs623736	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs625054	0.93[EUR][1000 genomes]
rs630099	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs632526	0.95[EUR][1000 genomes]
rs635627	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs636367	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs637348	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647744	0.81[AMR][1000 genomes]
rs648664	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs649933	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs650555	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs666199	0.81[AMR][1000 genomes]
rs669469	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs669890	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs674575	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs680108	0.80[AMR][1000 genomes]
rs683944	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS 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	8 gene(s)	inside rSNPs	diseases
2	nsv1022965	chr6:145374851-145635385	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830834	chr6:145392073-145556294	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs559299	STX11	cis	cerebellum	SCAN
rs559299	EPM2A	cis	parietal	SCAN
rs559299	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145430600-145434400	Enhancers	HMEC	breast
2	chr6:145430800-145432000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr6:145430800-145433400	Enhancers	NHEK	skin
4	chr6:145430800-145434400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:145431200-145431600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:145431200-145431600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:145431200-145433400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:145431200-145433400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:145431400-145431600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:145431400-145431600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:145431400-145431600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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