Variant report

Variant	rs2425516
Chromosome Location	chr20:41306600-41306601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12479621	0.81[CEU][hapmap]
rs16987210	0.81[CEU][hapmap]
rs2206427	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2206428	0.81[CEU][hapmap]
rs2206429	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2223540	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs2425509	0.93[EUR][1000 genomes]
rs2425512	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2425513	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2425520	0.81[CEU][hapmap]
rs2425524	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2425537	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2867493	0.81[CEU][hapmap]
rs2867494	0.81[CEU][hapmap]
rs3091699	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3092136	0.96[CEU][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs3092592	0.81[CEU][hapmap]
rs3092656	0.82[JPT][hapmap]
rs4810363	0.81[CEU][hapmap]
rs4810364	0.81[CEU][hapmap]
rs4810365	0.81[CEU][hapmap]
rs4810366	0.81[CEU][hapmap]
rs4810367	0.87[CEU][hapmap]
rs4812613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4812621	0.81[CEU][hapmap]
rs4812622	0.81[CEU][hapmap]
rs4812623	0.81[CEU][hapmap]
rs4812624	0.81[CEU][hapmap]
rs4812625	0.81[CEU][hapmap]
rs4812626	0.81[CEU][hapmap]
rs4812629	0.80[CEU][hapmap]
rs4812631	0.81[CEU][hapmap]
rs4812632	0.81[CEU][hapmap]
rs6016864	1.00[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6030406	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6065525	0.81[CEU][hapmap]
rs6072819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6072824	0.81[CEU][hapmap]
rs6072826	0.81[CEU][hapmap]
rs6072833	0.81[CEU][hapmap]
rs6102976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6102985	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6102992	0.86[EUR][1000 genomes]
rs926482	0.96[CEU][hapmap];0.85[EUR][1000 genomes]

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	nsv1064253	chr20:41120425-41379706	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv532517	chr20:41188651-41342196	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv949644	chr20:41207365-41333541	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv912878	chr20:41222480-41361424	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv833988	chr20:41227788-41379921	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1058990	chr20:41289969-41543912	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv544277	chr20:41289969-41543912	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv586028	chr20:41296994-41381215	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2425516	TNNC2	cis	cerebellum	SCAN
rs2425516	SNORA71B	cis	parietal	SCAN
rs2425516	SPINT3	cis	cerebellum	SCAN
rs2425516	PCIF1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41303800-41306600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:41304000-41309600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr20:41305000-41306800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:41305800-41306600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr20:41306200-41306600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:41306600-41306800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:41306600-41306800	Enhancers	Pancreas	Pancrea
8	chr20:41306600-41313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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