Variant report

Variant	rs12965829
Chromosome Location	chr18:28809685-28809686
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	chr18:28787689..28790379-chr18:28808328..28810205,2	MCF-7	breast:

Extended variants
information (count: 163 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10164077	1.00[CHB][hapmap]
rs10438930	1.00[CHB][hapmap]
rs11081691	1.00[CHB][hapmap]
rs1154850	1.00[CHB][hapmap]
rs11659665	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11660638	0.88[EUR][1000 genomes]
rs11663622	1.00[CHB][hapmap]
rs11663676	1.00[CHB][hapmap]
rs11663924	0.80[EUR][1000 genomes]
rs11664596	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11872734	1.00[CHB][hapmap]
rs11873223	0.82[EUR][1000 genomes]
rs11873281	0.80[EUR][1000 genomes]
rs11875510	1.00[CHB][hapmap]
rs11875560	1.00[CHB][hapmap]
rs12606446	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12606722	0.90[EUR][1000 genomes]
rs12607370	1.00[CHB][hapmap]
rs12957659	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958069	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958073	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958351	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958377	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12959058	0.90[EUR][1000 genomes]
rs12962355	1.00[CHB][hapmap]
rs12963302	1.00[CHB][hapmap]
rs12964422	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964443	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964839	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12964907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965177	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12966119	1.00[JPT][hapmap]
rs12967407	1.00[CHB][hapmap]
rs12969200	1.00[CHB][hapmap]
rs1426309	1.00[CHB][hapmap]
rs1426310	1.00[CHB][hapmap]
rs1426311	1.00[CHB][hapmap]
rs1544880	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1593511	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17658464	0.89[EUR][1000 genomes]
rs17715828	1.00[CHB][hapmap]
rs2007149	1.00[CHB][hapmap]
rs2042720	0.90[EUR][1000 genomes]
rs2114269	1.00[CHB][hapmap]
rs2162273	1.00[CHB][hapmap]
rs2162274	0.90[EUR][1000 genomes]
rs2199301	1.00[CHB][hapmap]
rs2219583	1.00[CHB][hapmap]
rs28372393	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28510667	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28615832	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28633353	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901124	1.00[CHB][hapmap]
rs2901125	1.00[CHB][hapmap]
rs34187983	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212801	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34301793	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34530511	0.90[EUR][1000 genomes]
rs34634416	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664857	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743470	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35136508	0.89[EUR][1000 genomes]
rs35220971	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35223713	0.80[EUR][1000 genomes]
rs35229932	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35257713	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35287825	0.82[EUR][1000 genomes]
rs35362621	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35596545	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909227	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810007	1.00[CHB][hapmap]
rs3810008	1.00[CHB][hapmap]
rs4349226	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356544	1.00[CHB][hapmap]
rs4408611	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4517864	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4539673	0.90[EUR][1000 genomes]
rs4598984	0.87[EUR][1000 genomes]
rs55776955	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778425	0.80[EUR][1000 genomes]
rs55965644	0.80[EUR][1000 genomes]
rs56088904	0.81[EUR][1000 genomes]
rs56308568	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62087700	0.91[EUR][1000 genomes]
rs62087701	0.90[EUR][1000 genomes]
rs62087702	0.90[EUR][1000 genomes]
rs62087703	0.90[EUR][1000 genomes]
rs62088665	0.82[EUR][1000 genomes]
rs62090396	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62090401	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506899	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506903	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6506904	0.90[EUR][1000 genomes]
rs6506914	1.00[CHB][hapmap]
rs6506916	1.00[CHB][hapmap]
rs67014182	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67550130	0.82[EUR][1000 genomes]
rs7226461	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7227412	0.80[EUR][1000 genomes]
rs7229569	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7230461	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7231460	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7232206	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7233743	1.00[CHB][hapmap]
rs7234662	1.00[CHB][hapmap]
rs7234854	1.00[CHB][hapmap]
rs7235354	1.00[CHB][hapmap]
rs7235384	0.90[EUR][1000 genomes]
rs7235951	1.00[CHB][hapmap]
rs7235975	1.00[CHB][hapmap]
rs7236225	1.00[CHB][hapmap]
rs7237370	1.00[CHB][hapmap]
rs7237383	1.00[CHB][hapmap]
rs7237419	1.00[CHB][hapmap]
rs7239695	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7240897	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7241874	0.80[EUR][1000 genomes]
rs7242742	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7243151	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243262	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243638	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243885	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243922	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243984	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244015	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244050	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244153	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244510	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245008	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72914749	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765054	1.00[CHB][hapmap]
rs8087103	0.90[EUR][1000 genomes]
rs8087410	1.00[CHB][hapmap]
rs8087786	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8088637	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8088973	0.93[EUR][1000 genomes]
rs8089598	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8089762	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8091151	1.00[CHB][hapmap]
rs8091579	1.00[CHB][hapmap]
rs8091715	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8091847	1.00[CHB][hapmap]
rs8091871	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs966376	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9946611	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9947296	0.82[CHB][hapmap]
rs9947444	1.00[CHB][hapmap]
rs9948210	1.00[CHB][hapmap]
rs9950209	1.00[CHB][hapmap]
rs9950622	1.00[CHB][hapmap]
rs9950769	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950949	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950971	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951016	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951341	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs9956026	1.00[CHB][hapmap]
rs9957758	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9963626	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12965829	TTR	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28805000-28811000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:28806000-28810400	Weak transcription	Hela-S3	cervix
3	chr18:28806200-28809800	Weak transcription	A549	lung
4	chr18:28806200-28812200	Weak transcription	Pancreas	Pancrea
5	chr18:28806400-28809800	Weak transcription	NH-A	brain
6	chr18:28806600-28809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:28807400-28812400	Weak transcription	Left Ventricle	heart
8	chr18:28807800-28813600	Weak transcription	Stomach Mucosa	stomach
9	chr18:28808200-28813200	Weak transcription	Fetal Heart	heart
10	chr18:28808600-28809800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr18:28809000-28810000	Flanking Active TSS	Liver	Liver
12	chr18:28809000-28810400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr18:28809200-28810400	Enhancers	HMEC	breast
14	chr18:28809400-28811400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr18:28809400-28811600	Enhancers	NHEK	skin
16	chr18:28809600-28810600	Flanking Active TSS	GM12878-XiMat	blood
17	chr18:28809600-28811400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr18:28809600-28811600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr18:28809600-28812600	Enhancers	HepG2	liver
20	chr18:28809600-28813800	Enhancers	Fetal Intestine Large	intestine
21	chr18:28809600-28813800	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links