Variant report

Variant	rs3825404
Chromosome Location	chr12:48399931-48399932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48392370..48394722-chr12:48397446..48401400,3	K562	blood:
2	chr12:48399203..48400811-chr12:48412734..48415114,2	K562	blood:
3	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:
4	chr12:48399203..48401006-chr12:48440249..48442960,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL2A1-1	chr12:48399838-48399995	ENSG00000258203

No data

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1018973	0.81[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs1034762	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs10492080	0.92[TSI][hapmap]
rs10783226	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612578	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs11612970	0.81[EUR][1000 genomes]
rs11613485	0.81[CEU][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs12580764	0.82[EUR][1000 genomes]
rs1476608	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs1635526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1635528	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635529	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635534	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1635535	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1635550	0.81[CHB][hapmap]
rs17122611	0.82[EUR][1000 genomes]
rs17122612	0.81[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs17122613	0.81[EUR][1000 genomes]
rs17122651	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs1793912	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1793913	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1793915	0.81[AMR][1000 genomes]
rs1793917	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1793931	0.94[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793933	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793955	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793956	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1859441	0.87[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs1859444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968071	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs1990029	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286022	0.85[EUR][1000 genomes]
rs3742074	0.81[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3803182	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3803183	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803184	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4293182	0.80[EUR][1000 genomes]
rs4760611	0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4760614	0.88[EUR][1000 genomes]
rs4760615	0.89[EUR][1000 genomes]
rs4760618	0.89[EUR][1000 genomes]
rs4760620	0.88[TSI][hapmap]
rs4760677	0.88[EUR][1000 genomes]
rs4760683	0.88[TSI][hapmap]
rs57380031	0.81[EUR][1000 genomes]
rs59766465	0.81[EUR][1000 genomes]
rs60629297	0.81[EUR][1000 genomes]
rs60681522	0.82[EUR][1000 genomes]
rs6580647	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580649	1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs6580651	0.88[EUR][1000 genomes]
rs7132668	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7133249	0.82[EUR][1000 genomes]
rs726354	0.92[TSI][hapmap]
rs72644841	0.92[EUR][1000 genomes]
rs72644842	0.88[EUR][1000 genomes]
rs72644843	0.82[EUR][1000 genomes]
rs72644844	0.82[EUR][1000 genomes]
rs7296913	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs7305954	0.83[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310579	0.89[EUR][1000 genomes]
rs7315258	0.88[TSI][hapmap]
rs7957764	0.89[EUR][1000 genomes]
rs7959755	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs7967762	0.81[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs7971668	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs917055	0.87[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9651993	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9805048	0.83[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3825404	ZNF641	cis	Whole Blood	GTEx
rs3825404	AQP2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399000-48400200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:48399200-48400000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:48399200-48400200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48399400-48400000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:48399400-48400000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
7	chr12:48399800-48400000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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