Variant report

Variant	rs1507108
Chromosome Location	chr6:54594968-54594969
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54594502..54597427-chr6:54632424..54633945,2	MCF-7	breast:
2	chr6:54591002..54596706-chr6:54709941..54714732,14	MCF-7	breast:
3	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
4	chr6:54588605..54590894-chr6:54594243..54596836,3	MCF-7	breast:
5	chr6:54585837..54588493-chr6:54594744..54597239,2	MCF-7	breast:
6	chr6:54589684..54593022-chr6:54593846..54596999,3	MCF-7	breast:
7	chr6:54594451..54596147-chr6:54739921..54742591,2	MCF-7	breast:
8	chr6:54594616..54597518-chr6:54631395..54633965,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12664791	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs16885880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17682328	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs17682340	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2174144	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57404514	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60228786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62414271	0.86[EUR][1000 genomes]
rs62414312	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62414315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62414316	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62414318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62414319	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62414351	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62414352	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62414354	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7757553	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9474936	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv885901	chr6:54588069-54635417	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885902	chr6:54588069-54656673	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1507108	AKAP7	trans	lymphoblastoid	seeQTL
rs1507108	NTS	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54594200-54595000	Enhancers	HMEC	breast
2	chr6:54594200-54595200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:54594200-54595600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:54594400-54595000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54594400-54595600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:54594600-54595600	Enhancers	Fetal Intestine Small	intestine
7	chr6:54594800-54595000	Flanking Active TSS	NHEK	skin
8	chr6:54594800-54595400	Enhancers	Rectal Mucosa Donor 31	rectum

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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