Variant report

Variant	rs544904
Chromosome Location	chr6:145433780-145433781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1007379	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13192528	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2328639	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2761089	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2788713	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2788720	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs477572	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs480110	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs499988	0.95[EUR][1000 genomes]
rs510141	0.96[EUR][1000 genomes]
rs512985	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514258	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs515224	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs519680	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs521471	0.95[EUR][1000 genomes]
rs526564	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs529733	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs539661	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540319	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559299	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs561083	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs565687	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs572490	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584911	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs605757	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs607623	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609639	0.99[EUR][1000 genomes]
rs620561	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621529	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs623736	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs625054	0.95[EUR][1000 genomes]
rs630099	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs632526	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs635627	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs636367	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637348	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs648664	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649933	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650555	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs669469	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs669890	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs674575	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs683944	0.83[AMR][1000 genomes];0.99[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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1022965	chr6:145374851-145635385	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830834	chr6:145392073-145556294	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs544904	EPM2A	cis	parietal	SCAN
rs544904	PLAGL1	cis	cerebellum	SCAN
rs544904	STX11	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145430600-145434400	Enhancers	HMEC	breast
2	chr6:145430800-145434400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:145431800-145433800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:145433200-145433800	Enhancers	Liver	Liver
5	chr6:145433400-145437400	Weak transcription	NHEK	skin
6	chr6:145433600-145434400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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