Variant report

Variant	rs16872628
Chromosome Location	chr6:12313395-12313396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12311955..12317813-chr6:12323964..12327057,7	MCF-7	breast:
2	chr6:12313162..12315409-chr6:12364413..12366976,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16872592	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16872602	0.87[EUR][1000 genomes]
rs16872650	1.00[CEU][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872653	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872679	0.83[AMR][1000 genomes]
rs6899673	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6906760	0.96[EUR][1000 genomes]
rs7356986	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7760229	0.83[AMR][1000 genomes]
rs9296345	0.92[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9471435	0.96[EUR][1000 genomes]
rs9471486	0.83[AMR][1000 genomes]
rs9471496	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16872628	TBC1D7	cis	parietal	SCAN
rs16872628	TBC1D7	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12296600-12314400	Weak transcription	Spleen	Spleen
2	chr6:12311600-12314200	Weak transcription	Pancreas	Pancrea
3	chr6:12311800-12313600	Weak transcription	Stomach Mucosa	stomach
4	chr6:12312200-12315200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:12312800-12313400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:12312800-12313600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr6:12312800-12315200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:12313000-12313600	Enhancers	NHEK	skin
9	chr6:12313000-12313800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:12313000-12313800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:12313000-12313800	Flanking Active TSS	A549	lung
12	chr6:12313000-12313800	Enhancers	HUVEC	blood vessel
13	chr6:12313000-12314000	Enhancers	Osteobl	bone
14	chr6:12313000-12314400	Enhancers	Fetal Heart	heart
15	chr6:12313000-12314400	Enhancers	HMEC	breast
16	chr6:12313000-12314600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:12313000-12315000	Enhancers	Placenta	Placenta
18	chr6:12313000-12315200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:12313200-12314200	Enhancers	NHDF-Ad	bronchial
20	chr6:12313200-12314400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:12313200-12314400	Weak transcription	NH-A	brain
22	chr6:12313200-12315200	Enhancers	HSMMtube	muscle
23	chr6:12313200-12315600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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