Variant report

Variant	rs2449278
Chromosome Location	chr1:225203408-225203409
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225202258..225204234-chr8:111898982..111900583,2	MCF-7	breast:

Extended variants
information (count: 234 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:227)

rs_ID	r²[population]
rs10399959	1.00[EUR][1000 genomes]
rs10495232	1.00[EUR][1000 genomes]
rs1078794	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10915724	1.00[EUR][1000 genomes]
rs10915732	1.00[EUR][1000 genomes]
rs11805350	1.00[EUR][1000 genomes]
rs12059834	1.00[EUR][1000 genomes]
rs12061265	1.00[EUR][1000 genomes]
rs12066443	1.00[EUR][1000 genomes]
rs12069808	1.00[EUR][1000 genomes]
rs12071270	1.00[EUR][1000 genomes]
rs12071776	1.00[EUR][1000 genomes]
rs12074382	1.00[EUR][1000 genomes]
rs12075769	1.00[EUR][1000 genomes]
rs12079808	1.00[EUR][1000 genomes]
rs12080062	1.00[EUR][1000 genomes]
rs12086473	1.00[EUR][1000 genomes]
rs12097593	1.00[EUR][1000 genomes]
rs12239937	1.00[EUR][1000 genomes]
rs13376360	1.00[EUR][1000 genomes]
rs1395115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1480102	1.00[EUR][1000 genomes]
rs1482279	0.82[AFR][1000 genomes]
rs1580956	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16844321	1.00[EUR][1000 genomes]
rs16844324	1.00[EUR][1000 genomes]
rs16844328	1.00[EUR][1000 genomes]
rs16844331	1.00[EUR][1000 genomes]
rs16844347	1.00[EUR][1000 genomes]
rs16844357	1.00[EUR][1000 genomes]
rs16855953	1.00[EUR][1000 genomes]
rs16856828	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1905114	0.82[AFR][1000 genomes]
rs2127558	1.00[EUR][1000 genomes]
rs2153246	1.00[EUR][1000 genomes]
rs2244108	1.00[EUR][1000 genomes]
rs2244109	1.00[EUR][1000 genomes]
rs2244198	1.00[EUR][1000 genomes]
rs2245097	1.00[EUR][1000 genomes]
rs2254430	1.00[EUR][1000 genomes]
rs2449262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449264	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449265	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449267	0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449268	0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449270	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449272	0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449273	0.84[AFR][1000 genomes]
rs2449274	0.84[AFR][1000 genomes]
rs2449275	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449276	0.85[AFR][1000 genomes]
rs2449277	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449279	1.00[EUR][1000 genomes]
rs2449280	0.85[AFR][1000 genomes]
rs2449283	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449284	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449286	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449288	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449289	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449290	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449292	0.81[AFR][1000 genomes]
rs2449294	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449302	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449305	1.00[EUR][1000 genomes]
rs2449306	1.00[EUR][1000 genomes]
rs2449309	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449311	0.84[AFR][1000 genomes]
rs2449312	0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449313	0.84[AFR][1000 genomes]
rs2449314	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449317	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449319	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449321	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449323	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2449324	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2456335	0.84[AFR][1000 genomes]
rs2456338	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2456339	0.84[AFR][1000 genomes]
rs2456340	0.84[AFR][1000 genomes]
rs2456343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2456344	1.00[EUR][1000 genomes]
rs2456346	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2456350	1.00[EUR][1000 genomes]
rs2456352	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2456354	1.00[EUR][1000 genomes]
rs2489299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489305	1.00[EUR][1000 genomes]
rs2489307	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489309	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489315	0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489316	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489317	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489318	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489319	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489322	0.82[AFR][1000 genomes]
rs2489323	0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489325	0.81[AFR][1000 genomes]
rs2489326	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489328	0.81[AFR][1000 genomes]
rs2489329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489330	0.81[AFR][1000 genomes]
rs2489331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489332	0.81[AFR][1000 genomes]
rs2489333	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489335	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489339	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489342	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489345	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489347	0.95[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489349	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489350	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489351	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489354	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489356	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489357	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489358	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2489359	1.00[EUR][1000 genomes]
rs2489360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501065	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501067	0.82[AFR][1000 genomes]
rs2501069	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2501074	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501076	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501077	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501079	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501080	0.91[AMR][1000 genomes]
rs2501088	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501103	1.00[EUR][1000 genomes]
rs2501104	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501112	1.00[EUR][1000 genomes]
rs2501113	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501117	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501121	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2501123	0.85[AFR][1000 genomes]
rs2501124	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501125	0.81[AFR][1000 genomes]
rs2501128	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501129	0.82[AFR][1000 genomes]
rs2501130	0.82[AFR][1000 genomes]
rs2501136	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501137	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501142	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501144	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501148	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501152	0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2501157	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2516334	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2662910	1.00[EUR][1000 genomes]
rs2662911	1.00[EUR][1000 genomes]
rs2662913	1.00[EUR][1000 genomes]
rs2802546	1.00[EUR][1000 genomes]
rs2802547	1.00[EUR][1000 genomes]
rs2802567	1.00[EUR][1000 genomes]
rs2802736	1.00[EUR][1000 genomes]
rs28789844	1.00[EUR][1000 genomes]
rs28871966	1.00[EUR][1000 genomes]
rs2929627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929629	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929632	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2939367	0.89[AFR][1000 genomes]
rs3102105	1.00[EUR][1000 genomes]
rs3128647	0.83[AMR][1000 genomes]
rs3991375	1.00[EUR][1000 genomes]
rs4121159	1.00[EUR][1000 genomes]
rs4256778	1.00[EUR][1000 genomes]
rs4275419	1.00[EUR][1000 genomes]
rs4475714	1.00[EUR][1000 genomes]
rs4639722	1.00[EUR][1000 genomes]
rs58205526	1.00[EUR][1000 genomes]
rs58355180	1.00[EUR][1000 genomes]
rs58651151	1.00[EUR][1000 genomes]
rs58823550	1.00[EUR][1000 genomes]
rs59730608	1.00[EUR][1000 genomes]
rs59730777	1.00[EUR][1000 genomes]
rs59839860	1.00[EUR][1000 genomes]
rs60434067	1.00[EUR][1000 genomes]
rs60727542	1.00[EUR][1000 genomes]
rs61269802	1.00[EUR][1000 genomes]
rs61329501	1.00[EUR][1000 genomes]
rs61483735	1.00[EUR][1000 genomes]
rs6426164	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656178	1.00[EUR][1000 genomes]
rs6666664	1.00[EUR][1000 genomes]
rs6670335	1.00[EUR][1000 genomes]
rs6673779	1.00[EUR][1000 genomes]
rs6675157	1.00[EUR][1000 genomes]
rs6675162	1.00[EUR][1000 genomes]
rs6680659	1.00[EUR][1000 genomes]
rs6683197	1.00[EUR][1000 genomes]
rs6689608	1.00[EUR][1000 genomes]
rs6693680	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6694400	1.00[EUR][1000 genomes]
rs6698293	1.00[EUR][1000 genomes]
rs6698942	1.00[EUR][1000 genomes]
rs6699883	1.00[EUR][1000 genomes]
rs73129804	1.00[EUR][1000 genomes]
rs7418261	1.00[EUR][1000 genomes]
rs7515136	1.00[EUR][1000 genomes]
rs7523371	1.00[EUR][1000 genomes]
rs7524227	1.00[EUR][1000 genomes]
rs7525497	1.00[EUR][1000 genomes]
rs7526764	1.00[EUR][1000 genomes]
rs7533311	1.00[EUR][1000 genomes]
rs7533415	1.00[EUR][1000 genomes]
rs7535962	1.00[EUR][1000 genomes]
rs7536912	1.00[EUR][1000 genomes]
rs7537947	1.00[EUR][1000 genomes]
rs7544960	1.00[EUR][1000 genomes]
rs7555397	1.00[EUR][1000 genomes]
rs769297	1.00[EUR][1000 genomes]
rs9286991	1.00[EUR][1000 genomes]
rs9426101	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9426103	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9426104	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9426147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9426156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9426159	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9660934	1.00[EUR][1000 genomes]
rs9725252	1.00[EUR][1000 genomes]
rs9803691	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757773	chr1:225087924-225253274	Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2759001	chr1:225087924-225253274	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3438976	chr1:225133567-225248753	Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1804634	chr1:225137134-225206826	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv873225	chr1:225162060-225373936	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv549262	chr1:225191852-225319898	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv549263	chr1:225202426-225319898	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225187000-225203600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:225199400-225207000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:225201200-225206200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:225201400-225203600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr1:225202000-225203600	Weak transcription	Pancreas	Pancrea
6	chr1:225202000-225205200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:225202200-225203800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr1:225202200-225204800	Weak transcription	Fetal Stomach	stomach
9	chr1:225202800-225204000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:225202800-225204800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:225203400-225203800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:225203400-225203800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:225203400-225203800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr1:225203400-225203800	ZNF genes & repeats	Ovary	ovary
15	chr1:225203400-225204000	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr1:225203400-225205000	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links