Variant report

Variant	rs16939839
Chromosome Location	chr15:58459075-58459076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58451875..58456386-chr15:58457557..58459744,5	K562	blood:
2	chr15:58452711..58455369-chr15:58457890..58460728,2	MCF-7	breast:
3	chr15:58451875..58454675-chr15:58458002..58459744,2	K562	blood:
4	chr15:58457163..58460249-chr15:58468233..58471898,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1317851	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17240643	0.88[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs17240650	0.90[CEU][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs17240671	0.86[EUR][1000 genomes]
rs17821086	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17821117	0.88[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1814461	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271678	0.90[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2292714	0.94[EUR][1000 genomes]
rs2414537	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2414538	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414539	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2414543	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414544	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414545	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784248	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784255	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3825777	0.90[EUR][1000 genomes]
rs4643260	0.87[EUR][1000 genomes]
rs55832939	0.90[EUR][1000 genomes]
rs55860231	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55885730	0.90[EUR][1000 genomes]
rs56141765	0.90[EUR][1000 genomes]
rs61113628	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66717621	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66881380	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66896776	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67670862	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67683432	0.87[EUR][1000 genomes]
rs7161943	0.87[EUR][1000 genomes]
rs7165818	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7165997	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7179531	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7181378	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737450	0.86[EUR][1000 genomes]
rs72743586	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7496709	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs935204	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16939839	CGNL1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58441000-58463800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:58451200-58481000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:58454800-58471400	Weak transcription	Spleen	Spleen
4	chr15:58455600-58461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:58457400-58459800	Enhancers	Fetal Heart	heart
6	chr15:58457600-58459200	Enhancers	K562	blood
7	chr15:58457800-58461200	Enhancers	HepG2	liver
8	chr15:58458400-58459800	Enhancers	Brain Germinal Matrix	brain
9	chr15:58458400-58463400	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:58458400-58477800	Strong transcription	Liver	Liver
11	chr15:58458800-58459200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:58459000-58459800	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links