Variant report

Variant	rs2569146
Chromosome Location	chr5:127096801-127096802
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	chr5:127096123..127098291-chr5:127100093..127102931,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10041967	0.82[EUR][1000 genomes]
rs10061252	0.81[EUR][1000 genomes]
rs1007623	0.82[EUR][1000 genomes]
rs10519953	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs10519960	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1086523	0.81[EUR][1000 genomes]
rs1086525	0.81[EUR][1000 genomes]
rs1086526	0.81[EUR][1000 genomes]
rs1086527	0.83[EUR][1000 genomes]
rs1086529	0.81[EUR][1000 genomes]
rs1086530	0.80[EUR][1000 genomes]
rs1086531	0.83[EUR][1000 genomes]
rs1086532	0.83[EUR][1000 genomes]
rs1086533	0.81[EUR][1000 genomes]
rs1086534	0.82[EUR][1000 genomes]
rs1088167	0.81[EUR][1000 genomes]
rs10900792	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1092720	0.81[EUR][1000 genomes]
rs11241938	0.82[EUR][1000 genomes]
rs11241939	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11241942	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11950864	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11957799	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1213827	0.82[EUR][1000 genomes]
rs1228156	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234542	0.82[EUR][1000 genomes]
rs12652197	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12653785	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1399829	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1421747	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1432958	0.83[EUR][1000 genomes]
rs1515640	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560673	0.95[CEU][hapmap];0.88[TSI][hapmap]
rs173580	0.82[EUR][1000 genomes]
rs173581	0.83[EUR][1000 genomes]
rs173582	0.81[EUR][1000 genomes]
rs1816404	0.82[EUR][1000 genomes]
rs1816405	0.82[EUR][1000 genomes]
rs1849938	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs187461	0.82[EUR][1000 genomes]
rs1897525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193736	0.82[EUR][1000 genomes]
rs248689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap]
rs248692	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[TSI][hapmap]
rs248709	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs248711	0.83[EUR][1000 genomes]
rs248712	0.81[EUR][1000 genomes]
rs248713	0.83[EUR][1000 genomes]
rs248715	0.81[EUR][1000 genomes]
rs248716	0.85[EUR][1000 genomes]
rs248717	0.83[EUR][1000 genomes]
rs248718	0.82[EUR][1000 genomes]
rs248720	0.81[EUR][1000 genomes]
rs248721	0.81[EUR][1000 genomes]
rs248722	0.84[EUR][1000 genomes]
rs248724	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs248730	0.82[EUR][1000 genomes]
rs248731	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248732	0.82[EUR][1000 genomes]
rs248733	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248735	0.82[EUR][1000 genomes]
rs248737	0.81[EUR][1000 genomes]
rs248738	0.82[EUR][1000 genomes]
rs248739	0.82[EUR][1000 genomes]
rs248740	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248741	0.82[EUR][1000 genomes]
rs248742	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2569142	0.83[EUR][1000 genomes]
rs2569144	0.83[EUR][1000 genomes]
rs2569148	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2673749	0.82[EUR][1000 genomes]
rs2673750	0.81[EUR][1000 genomes]
rs2673763	0.83[EUR][1000 genomes]
rs2673772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4361571	0.81[EUR][1000 genomes]
rs54201	0.82[EUR][1000 genomes]
rs57883466	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59513079	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62373501	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62373502	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6595789	0.85[EUR][1000 genomes]
rs7714847	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs790827	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791071	0.81[EUR][1000 genomes]
rs791072	0.81[EUR][1000 genomes]
rs791073	0.81[EUR][1000 genomes]
rs791074	0.83[EUR][1000 genomes]
rs809349	0.81[EUR][1000 genomes]
rs812059	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs899190	0.81[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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830480	chr5:126964751-127124522	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2569146	SLC12A2	cis	cerebellum	SCAN
rs2569146	LYRM7	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127090200-127097000	Weak transcription	Fetal Lung	lung
2	chr5:127090800-127102400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:127093800-127098000	Weak transcription	Small Intestine	intestine
4	chr5:127093800-127098200	Weak transcription	Psoas Muscle	Psoas
5	chr5:127094000-127098000	Weak transcription	Brain Angular Gyrus	brain
6	chr5:127094000-127101800	Weak transcription	HUVEC	blood vessel
7	chr5:127094400-127097800	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:127095000-127098200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:127095200-127097800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:127095200-127102800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:127095600-127097800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:127096400-127099800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:127096600-127099000	Enhancers	Brain Hippocampus Middle	brain
14	chr5:127096600-127099000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:127096800-127097200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:127096800-127097800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:127096800-127097800	Enhancers	Brain Substantia Nigra	brain

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