Variant report

Variant	rs2739430
Chromosome Location	chr19:51516345-51516346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51516265-51516555	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:51516136-51516561	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:51512058..51513939-chr19:51514740..51518594,3	K562	blood:

Variant related genes	Relation type
ENSG00000268739	TF binding region
ENSG00000269741	TF binding region
KLK9	TF binding region
ENSG00000213022	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2075687	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075688	0.80[EUR][1000 genomes]
rs2075689	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2075690	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075691	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075693	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2075695	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2569448	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2569449	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2569451	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2691256	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2691258	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2739427	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2739431	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2739432	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2739433	0.83[EUR][1000 genomes]
rs2739434	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6509511	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6509512	0.88[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7250580	0.85[ASN][1000 genomes]
rs9524	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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	nsv912291	chr19:51505725-51537682	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2739430	CTC-518B2.12	cis	Skin Sun Exposed Lower leg	GTEx
rs2739430	LILRB1	cis	cerebellum	SCAN
rs2739430	RPL28	cis	parietal	SCAN
rs2739430	KLK10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51510200-51517000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr19:51514400-51519000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:51514600-51517200	Weak transcription	Esophagus	oesophagus
4	chr19:51514800-51517200	Weak transcription	NHEK	skin
5	chr19:51514800-51517400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:51514800-51517600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:51514800-51520200	Weak transcription	Right Atrium	heart
8	chr19:51516000-51517400	Weak transcription	Ovary	ovary
9	chr19:51516200-51516600	ZNF genes & repeats	HMEC	breast

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