Variant report

Variant	rs17240650
Chromosome Location	chr15:58479008-58479009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58260270..58262441-chr15:58476385..58479078,2	K562	blood:
2	chr15:58356916..58358526-chr15:58478594..58480634,2	K562	blood:
3	chr15:58471240..58473438-chr15:58477636..58480344,3	K562	blood:
4	chr15:58473604..58477327-chr15:58478403..58482264,4	K562	blood:

Variant related genes	Relation type
ENSG00000259285	Chromatin interaction
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1317851	0.84[EUR][1000 genomes]
rs16939839	0.90[EUR][1000 genomes]
rs17240643	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17240671	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17821086	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17821117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821135	0.85[EUR][1000 genomes]
rs1814461	0.84[EUR][1000 genomes]
rs2271678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292714	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2414537	0.84[EUR][1000 genomes]
rs2414538	0.84[EUR][1000 genomes]
rs2414539	0.84[EUR][1000 genomes]
rs2414543	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414544	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414545	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784248	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3784255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825777	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55672049	0.85[EUR][1000 genomes]
rs55808100	0.86[EUR][1000 genomes]
rs55832939	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55860231	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55885730	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56099208	0.89[EUR][1000 genomes]
rs56141765	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61113628	0.84[EUR][1000 genomes]
rs66717621	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66881380	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66896776	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67670862	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67683432	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7161943	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165818	0.84[EUR][1000 genomes]
rs7165997	0.84[EUR][1000 genomes]
rs7179531	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181378	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72737450	0.93[EUR][1000 genomes]
rs72743586	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7496709	0.83[EUR][1000 genomes]
rs935204	0.90[EUR][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	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2752813	chr15:58461006-58507064	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17240650	CGNL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58451200-58481000	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:58471600-58481200	Weak transcription	Right Atrium	heart
3	chr15:58475200-58481000	Weak transcription	K562	blood
4	chr15:58477800-58479400	Weak transcription	Liver	Liver
5	chr15:58478400-58481400	Weak transcription	GM12878-XiMat	blood
6	chr15:58478800-58483800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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