Variant report

Variant	rs16872602
Chromosome Location	chr6:12304829-12304830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16872592	0.88[EUR][1000 genomes]
rs16872628	0.87[EUR][1000 genomes]
rs16872650	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs16872653	0.84[EUR][1000 genomes]
rs6899673	0.88[EUR][1000 genomes]
rs6906760	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7356986	0.88[EUR][1000 genomes]
rs9296345	0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs9471435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9471441	0.89[ASN][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	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv525684	chr6:12301462-12307264	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16872602	TBC1D7	cis	cerebellum	SCAN
rs16872602	TBC1D7	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12296600-12314400	Weak transcription	Spleen	Spleen
2	chr6:12297200-12311200	Weak transcription	HUVEC	blood vessel
3	chr6:12298200-12305600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:12304000-12305600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:12304000-12306400	Enhancers	NHEK	skin
6	chr6:12304400-12305600	Enhancers	HMEC	breast
7	chr6:12304600-12306200	Genic enhancers	A549	lung
8	chr6:12304800-12305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:12304800-12306800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

Quick Search:

Input of quick search could be:

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

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