Variant report

Variant	rs9603621
Chromosome Location	chr13:40377353-40377354
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:40376872..40378665-chr13:40381947..40384768,2	MCF-7	breast:
2	chr13:40377104..40378017-chr13:40386019..40386823,2	MCF-7	breast:
3	chr13:40356408..40358571-chr13:40377020..40378591,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11617586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12019493	0.84[ASN][1000 genomes]
rs12020434	0.95[ASN][1000 genomes]
rs12857806	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12859245	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34927174	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4312181	0.92[ASN][1000 genomes]
rs4531603	0.97[ASN][1000 genomes]
rs4943700	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7317488	0.99[ASN][1000 genomes]
rs7335495	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988955	0.93[ASN][1000 genomes]
rs9594366	0.81[AMR][1000 genomes]
rs9594367	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9594368	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9603618	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9603619	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603620	0.97[ASN][1000 genomes]
rs9603626	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603627	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9603621	COG6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40374800-40378000	Weak transcription	Psoas Muscle	Psoas
2	chr13:40376400-40378400	Enhancers	Placenta	Placenta
3	chr13:40376800-40377800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:40376800-40378000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:40377200-40380000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr13:40377200-40380200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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