Variant report

Variant	rs12039969
Chromosome Location	chr1:221747913-221747914
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:221746909..221748850-chr1:221913979..221916326,2	MCF-7	breast:
2	chr1:221746709..221748888-chr1:221752322..221754674,2	K562	blood:
3	chr1:221746221..221748385-chr1:221914504..221916703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1026515	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10495169	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10495170	0.81[EUR][1000 genomes]
rs10779441	0.81[EUR][1000 genomes]
rs10779442	0.81[EUR][1000 genomes]
rs10779443	0.81[EUR][1000 genomes]
rs11118755	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118757	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118758	0.80[EUR][1000 genomes]
rs11118759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118764	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118772	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11118774	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12021531	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12026855	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12032922	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs12117680	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12118111	0.80[EUR][1000 genomes]
rs12142838	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12564947	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1338077	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538249	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1933266	0.81[EUR][1000 genomes]
rs1933267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009200	0.81[EUR][1000 genomes]
rs4129174	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs925944	0.81[EUR][1000 genomes]
rs9308400	0.81[EUR][1000 genomes]
rs953400	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9658820	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9658836	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9661910	0.81[EUR][1000 genomes]
rs9662660	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9725124	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9727407	0.81[EUR][1000 genomes]
rs9728231	0.81[EUR][1000 genomes]
rs9729646	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873200	chr1:221644180-221843191	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1009838	chr1:221692621-221773945	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535301	chr1:221692621-221773945	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1809909	chr1:221740539-221754260	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2760080	chr1:221742890-221763387	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3452707	chr1:221743835-221754556	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3452709	chr1:221743953-221754426	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv11257	chr1:221743956-221754422	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1808490	chr1:221743979-221779026	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv947470	chr1:221744072-221749422	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1804329	chr1:221746038-221753597	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1805310	chr1:221746038-221753597	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1807047	chr1:221746038-221756526	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv514046	chr1:221746049-221749329	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1806301	chr1:221746050-221753609	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1806766	chr1:221746050-221753609	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1807384	chr1:221746050-221753609	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv441739	chr1:221746050-221753609	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv2421475	chr1:221746050-221753645	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv1805810	chr1:221746140-221753981	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv1806865	chr1:221746140-221753981	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv1807648	chr1:221746140-221753981	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv1808522	chr1:221746140-221753981	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	esv1810177	chr1:221746140-221753981	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv1810412	chr1:221746140-221753981	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	esv1814839	chr1:221746140-221753981	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	esv1811498	chr1:221746140-221758568	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	esv1814250	chr1:221746140-221772404	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	esv1810033	chr1:221747848-221753597	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	esv1813773	chr1:221747848-221756526	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12039969	LYPLAL1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221729800-221748600	Weak transcription	Left Ventricle	heart
2	chr1:221729800-221748800	Weak transcription	Pancreas	Pancrea
3	chr1:221746600-221748800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr1:221746600-221749000	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr1:221746800-221749600	Enhancers	Fetal Heart	heart
6	chr1:221747400-221748200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:221747400-221748800	Weak transcription	Psoas Muscle	Psoas
8	chr1:221747800-221748000	Enhancers	Colon Smooth Muscle	Colon
9	chr1:221747800-221748800	Weak transcription	Fetal Muscle Leg	muscle

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