Variant report

Variant	rs2519540
Chromosome Location	chr12:119916900-119916901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:119614742..119619324-chr12:119914452..119918204,4	MCF-7	breast:
2	chr12:119913085..119915232-chr12:119915354..119917050,2	MCF-7	breast:
3	chr12:119882836..119888025-chr12:119914651..119920477,9	MCF-7	breast:
4	chr12:119915459..119919519-chr12:119922678..119926603,4	MCF-7	breast:
5	chr12:119894815..119897126-chr12:119915080..119916947,2	MCF-7	breast:
6	chr12:119883274..119886371-chr12:119915842..119918823,3	MCF-7	breast:
7	chr12:119881941..119882941-chr12:119916276..119917584,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000152137	Chromatin interaction

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

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

rs_ID	r²[population]
rs10774498	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1619163	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1620946	1.00[YRI][hapmap]
rs1622645	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs1716433	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716446	1.00[CEU][hapmap]
rs1727387	0.92[CEU][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1727390	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2519539	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2519542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695503	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2727742	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6490255	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs697892	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs708874	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs708875	1.00[YRI][hapmap]
rs708879	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs784841	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs784844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs784853	0.86[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs810784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047036	chr12:119477583-119992640	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv916688	chr12:119801814-120044407	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832529	chr12:119863378-120071646	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv3362333	chr12:119916369-119920867	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2519540	CDK18	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:119916800-119917000	Enhancers	HSMMtube	muscle
2	chr12:119916800-119917800	Enhancers	Placenta	Placenta
3	chr12:119916800-119918800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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