Variant report

Variant	rs2425562
Chromosome Location	chr20:41673335-41673336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1106978	0.80[JPT][hapmap]
rs206148	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs206150	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs206151	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs206152	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs206153	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs206154	0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs206155	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs206159	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs206162	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs206163	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2208048	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2208049	0.99[ASN][1000 genomes]
rs2425544	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2425545	0.93[ASN][1000 genomes]
rs2425546	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2425547	0.99[ASN][1000 genomes]
rs2425548	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2425549	0.97[ASN][1000 genomes]
rs2425550	0.99[ASN][1000 genomes]
rs2425551	0.99[ASN][1000 genomes]
rs2425552	0.99[ASN][1000 genomes]
rs2425553	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2425554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2425555	0.99[ASN][1000 genomes]
rs2425556	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2425557	0.99[ASN][1000 genomes]
rs2425558	0.99[ASN][1000 genomes]
rs2425559	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2425560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs2425561	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2425563	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs2425564	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2425565	0.99[ASN][1000 genomes]
rs2425566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2425567	0.80[JPT][hapmap]
rs2425568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2425570	0.80[JPT][hapmap]
rs2425572	0.83[JPT][hapmap];0.84[YRI][hapmap]
rs2425579	0.83[JPT][hapmap]
rs3091443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3091548	0.99[ASN][1000 genomes]
rs3091580	0.99[ASN][1000 genomes]
rs3091581	0.99[ASN][1000 genomes]
rs3091752	0.99[ASN][1000 genomes]
rs3091800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3091990	1.00[ASN][1000 genomes]
rs3091991	0.99[ASN][1000 genomes]
rs3092089	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3092095	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3092117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3092177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3092289	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3092292	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3092328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3092739	1.00[ASN][1000 genomes]
rs3092800	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4410343	0.82[ASN][1000 genomes]
rs4444608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4812667	0.82[ASN][1000 genomes]
rs6030610	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6030612	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6030613	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6030614	0.82[ASN][1000 genomes]
rs6030615	0.82[ASN][1000 genomes]
rs755149	0.83[JPT][hapmap]
rs8120802	0.82[ASN][1000 genomes]
rs910829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs910830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs927054	0.99[ASN][1000 genomes]
rs927055	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs927056	0.99[ASN][1000 genomes]
rs998739	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060468	chr20:41518010-41700012	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1061053	chr20:41521471-41704874	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv949221	chr20:41594025-41742176	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv869774	chr20:41595567-41746533	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2762078	chr20:41598181-41745491	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv948829	chr20:41598995-41742176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1061219	chr20:41613071-41673335	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1065908	chr20:41620966-41735969	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2425562	PABPC1L	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41671000-41673400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41672800-41673600	Enhancers	Fetal Brain Female	brain
3	chr20:41672800-41673800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr20:41672800-41673800	Enhancers	Fetal Brain Male	brain
5	chr20:41672800-41674000	Enhancers	Cortex derived primary cultured neurospheres	brain

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