Variant report

Variant	rs7752108
Chromosome Location	chr6:13997821-13997822
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13991753..13995333-chr6:13995809..14000536,6	K562	blood:
2	chr6:13995740..14002020-chr6:14004395..14009247,6	K562	blood:
3	chr6:13991412..13996106-chr6:13996876..14000522,5	K562	blood:
4	chr6:13990415..13992170-chr6:13995596..13998101,2	MCF-7	breast:
5	chr6:13996360..13998289-chr6:14000864..14003564,4	K562	blood:
6	chr6:13996360..13998267-chr6:14001201..14003560,3	K562	blood:

Variant related genes	Relation type
ENSG00000233981	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11757916	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1192057	0.90[CEU][hapmap]
rs12190765	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280152	0.85[CEU][hapmap]
rs280153	0.85[CEU][hapmap]
rs280154	0.85[CEU][hapmap]
rs280155	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280157	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280178	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280180	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs280181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280186	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280188	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs579538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs867204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9476344	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600995	chr6:13945067-14009231	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv600996	chr6:13954632-14014793	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7752108	NAV2	trans	brain	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13973400-14002400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:13978600-14001200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:13993600-13999400	Weak transcription	NHDF-Ad	bronchial
4	chr6:13993600-14001000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:13993600-14001200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:13994200-14000000	Weak transcription	Hela-S3	cervix
7	chr6:13995600-13999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:13995600-14000400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:13995600-14000400	Weak transcription	HMEC	breast
10	chr6:13995600-14001000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links