Variant report

Variant	rs788889
Chromosome Location	chr19:51311249-51311250
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:51309000..51310617-chr19:51310655..51313599,2	MCF-7	breast:
2	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
3	chr19:51159042..51161592-chr19:51310002..51312561,2	K562	blood:
4	chr19:51311248..51313298-chr19:51373951..51375653,2	K562	blood:
5	chr19:51311002..51313496-chr19:51319207..51321589,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167751	Chromatin interaction
ENSG00000167748	Chromatin interaction
ENSG00000180279	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10425724	0.85[ASN][1000 genomes]
rs1054713	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11672844	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197589	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1978605	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2247289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411334	0.90[ASN][1000 genomes]
rs2434449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456584	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2456585	0.97[ASN][1000 genomes]
rs2560931	0.97[ASN][1000 genomes]
rs2560933	0.97[ASN][1000 genomes]
rs2659058	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2659059	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659061	0.81[AFR][1000 genomes]
rs2659099	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2659100	0.90[ASN][1000 genomes]
rs2659101	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2659103	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2659104	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs266116	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs266122	0.97[ASN][1000 genomes]
rs266123	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs266125	0.97[ASN][1000 genomes]
rs266127	0.97[ASN][1000 genomes]
rs266128	0.92[ASN][1000 genomes]
rs5516	0.88[ASN][1000 genomes]
rs56164547	0.82[ASN][1000 genomes]
rs59524380	0.82[ASN][1000 genomes]
rs788886	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs788887	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs788890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv519121	chr19:51308092-51332670	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs788889	KLK1	cis	multi-tissue	Pritchard
rs788889	C19orf48	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51308800-51311400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:51308800-51311600	Weak transcription	Right Atrium	heart
3	chr19:51309200-51313600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:51309400-51311600	Weak transcription	Spleen	Spleen
5	chr19:51309600-51311800	Weak transcription	Pancreas	Pancrea

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