Variant report

Variant	rs1449888
Chromosome Location	chr3:17272276-17272277
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	chr3:16706868..16708588-chr3:17272260..17274832,2	MCF-7	breast:

Extended variants
information (count: 245 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:238)

rs_ID	r²[population]
rs10510475	0.89[EUR][1000 genomes]
rs10865749	0.87[EUR][1000 genomes]
rs1120412	0.87[EUR][1000 genomes]
rs11708391	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11713917	0.83[EUR][1000 genomes]
rs12488093	0.83[EUR][1000 genomes]
rs12488687	0.86[EUR][1000 genomes]
rs12493567	0.81[EUR][1000 genomes]
rs12494513	0.81[EUR][1000 genomes]
rs13093375	0.81[EUR][1000 genomes]
rs13318609	0.83[EUR][1000 genomes]
rs13318886	0.92[EUR][1000 genomes]
rs13322641	0.83[EUR][1000 genomes]
rs13353435	0.81[EUR][1000 genomes]
rs1374197	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1375817	0.90[EUR][1000 genomes]
rs1375818	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446303	0.87[EUR][1000 genomes]
rs1449879	0.90[EUR][1000 genomes]
rs1449881	0.89[EUR][1000 genomes]
rs1449882	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1449883	0.87[EUR][1000 genomes]
rs1449884	0.90[EUR][1000 genomes]
rs1449885	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449886	0.90[EUR][1000 genomes]
rs1449887	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463218	0.89[EUR][1000 genomes]
rs1463221	0.85[EUR][1000 genomes]
rs1463222	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1470667	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1545424	0.90[EUR][1000 genomes]
rs1597393	0.90[EUR][1000 genomes]
rs1597394	0.90[EUR][1000 genomes]
rs17043253	0.87[ASN][1000 genomes]
rs17043422	0.83[EUR][1000 genomes]
rs17043492	0.83[EUR][1000 genomes]
rs17043494	0.81[EUR][1000 genomes]
rs17043539	0.81[EUR][1000 genomes]
rs17043541	0.81[EUR][1000 genomes]
rs17200818	0.89[EUR][1000 genomes]
rs17200839	0.89[EUR][1000 genomes]
rs1867772	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs187303	0.85[EUR][1000 genomes]
rs2028874	0.89[EUR][1000 genomes]
rs2060623	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2060624	0.87[EUR][1000 genomes]
rs2060625	0.87[EUR][1000 genomes]
rs2060627	0.87[EUR][1000 genomes]
rs2060628	0.89[EUR][1000 genomes]
rs2060629	0.90[EUR][1000 genomes]
rs2084572	0.88[EUR][1000 genomes]
rs2121262	0.87[EUR][1000 genomes]
rs2122368	0.90[EUR][1000 genomes]
rs2167118	0.85[EUR][1000 genomes]
rs2167119	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2247106	0.89[EUR][1000 genomes]
rs2252237	0.90[EUR][1000 genomes]
rs2348001	0.87[EUR][1000 genomes]
rs2348003	0.89[EUR][1000 genomes]
rs2348004	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348005	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470347	0.88[EUR][1000 genomes]
rs2470577	0.88[EUR][1000 genomes]
rs2470580	0.83[EUR][1000 genomes]
rs2470581	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2470583	0.90[EUR][1000 genomes]
rs2592099	0.83[EUR][1000 genomes]
rs2596636	0.89[EUR][1000 genomes]
rs2596637	0.89[EUR][1000 genomes]
rs2596638	0.89[EUR][1000 genomes]
rs2596639	0.89[EUR][1000 genomes]
rs2596640	0.89[EUR][1000 genomes]
rs2596641	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596643	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2596645	0.89[EUR][1000 genomes]
rs2596646	0.89[EUR][1000 genomes]
rs2596647	0.89[EUR][1000 genomes]
rs2596648	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2596649	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2596650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2596652	0.83[EUR][1000 genomes]
rs2596655	0.83[EUR][1000 genomes]
rs2596656	0.83[EUR][1000 genomes]
rs2596657	0.85[EUR][1000 genomes]
rs2596658	0.85[EUR][1000 genomes]
rs2596662	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2596663	0.84[EUR][1000 genomes]
rs2596664	0.87[EUR][1000 genomes]
rs2596665	0.90[EUR][1000 genomes]
rs2596666	0.90[EUR][1000 genomes]
rs2596667	0.90[EUR][1000 genomes]
rs2596669	0.90[EUR][1000 genomes]
rs2596670	0.90[EUR][1000 genomes]
rs2596671	0.90[EUR][1000 genomes]
rs2596672	0.90[EUR][1000 genomes]
rs2596673	0.91[EUR][1000 genomes]
rs2596674	0.88[EUR][1000 genomes]
rs2596675	0.88[EUR][1000 genomes]
rs2596676	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2596677	0.87[EUR][1000 genomes]
rs2596678	0.88[EUR][1000 genomes]
rs2596679	0.88[EUR][1000 genomes]
rs2596680	0.88[EUR][1000 genomes]
rs2596681	0.88[EUR][1000 genomes]
rs2596682	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2733478	0.88[EUR][1000 genomes]
rs2733479	0.87[EUR][1000 genomes]
rs2733480	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2733481	0.88[EUR][1000 genomes]
rs2733485	0.88[EUR][1000 genomes]
rs2733486	0.85[EUR][1000 genomes]
rs2733487	0.88[EUR][1000 genomes]
rs2733489	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2733491	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733492	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2733493	0.89[EUR][1000 genomes]
rs2733494	0.89[EUR][1000 genomes]
rs2733495	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733496	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733497	0.89[EUR][1000 genomes]
rs2733498	0.90[EUR][1000 genomes]
rs2733499	0.90[EUR][1000 genomes]
rs2733500	0.90[EUR][1000 genomes]
rs2733501	0.90[EUR][1000 genomes]
rs2733502	0.90[EUR][1000 genomes]
rs2733504	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733507	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2733508	0.89[EUR][1000 genomes]
rs2733509	0.90[EUR][1000 genomes]
rs2733510	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2733514	0.88[EUR][1000 genomes]
rs2733515	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2733516	0.87[EUR][1000 genomes]
rs2733517	0.86[EUR][1000 genomes]
rs2733518	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733519	0.87[EUR][1000 genomes]
rs2733520	0.85[EUR][1000 genomes]
rs2733521	0.85[EUR][1000 genomes]
rs2733522	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2733523	0.88[EUR][1000 genomes]
rs2733524	0.88[EUR][1000 genomes]
rs2733525	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2733526	0.85[EUR][1000 genomes]
rs2733527	0.84[EUR][1000 genomes]
rs2733528	0.85[EUR][1000 genomes]
rs2733529	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2733530	0.85[EUR][1000 genomes]
rs283906	0.87[EUR][1000 genomes]
rs283907	0.87[EUR][1000 genomes]
rs283908	0.87[EUR][1000 genomes]
rs283909	0.87[EUR][1000 genomes]
rs283911	0.87[EUR][1000 genomes]
rs283912	0.87[EUR][1000 genomes]
rs283913	0.87[EUR][1000 genomes]
rs283914	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs283915	0.87[EUR][1000 genomes]
rs283916	0.87[EUR][1000 genomes]
rs283917	0.91[EUR][1000 genomes]
rs283918	0.88[EUR][1000 genomes]
rs283919	0.88[EUR][1000 genomes]
rs283921	0.87[EUR][1000 genomes]
rs283922	0.88[EUR][1000 genomes]
rs283923	0.88[EUR][1000 genomes]
rs283925	0.88[EUR][1000 genomes]
rs283927	0.85[EUR][1000 genomes]
rs283929	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs283930	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs283931	0.84[EUR][1000 genomes]
rs283934	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs283935	0.83[EUR][1000 genomes]
rs283936	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs283937	0.82[EUR][1000 genomes]
rs283938	0.85[EUR][1000 genomes]
rs283940	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs283941	0.85[EUR][1000 genomes]
rs283942	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs283943	0.85[EUR][1000 genomes]
rs283944	0.85[EUR][1000 genomes]
rs283945	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs283946	0.85[EUR][1000 genomes]
rs283947	0.85[EUR][1000 genomes]
rs283948	0.85[EUR][1000 genomes]
rs283949	0.85[EUR][1000 genomes]
rs28408438	0.83[EUR][1000 genomes]
rs28454413	0.83[EUR][1000 genomes]
rs34502358	0.83[EUR][1000 genomes]
rs35234876	0.81[EUR][1000 genomes]
rs35521582	0.81[EUR][1000 genomes]
rs4312642	0.89[EUR][1000 genomes]
rs4582042	0.82[EUR][1000 genomes]
rs4615062	0.81[EUR][1000 genomes]
rs58307801	0.85[EUR][1000 genomes]
rs62245860	0.86[EUR][1000 genomes]
rs62245914	0.83[EUR][1000 genomes]
rs62245947	0.82[EUR][1000 genomes]
rs6442679	0.83[EUR][1000 genomes]
rs6442680	0.81[EUR][1000 genomes]
rs6442682	0.87[EUR][1000 genomes]
rs6762516	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6763593	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6785870	0.83[EUR][1000 genomes]
rs6790367	0.88[ASN][1000 genomes]
rs6792443	0.88[EUR][1000 genomes]
rs6799259	0.81[EUR][1000 genomes]
rs6801690	0.89[EUR][1000 genomes]
rs6802891	0.83[EUR][1000 genomes]
rs723813	0.85[EUR][1000 genomes]
rs728022	0.89[EUR][1000 genomes]
rs7614318	0.88[EUR][1000 genomes]
rs7617933	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7623979	0.81[EUR][1000 genomes]
rs7625175	0.87[EUR][1000 genomes]
rs7625855	0.86[EUR][1000 genomes]
rs7630286	0.83[EUR][1000 genomes]
rs7630433	0.83[EUR][1000 genomes]
rs7636787	0.81[EUR][1000 genomes]
rs7642719	0.81[EUR][1000 genomes]
rs7645756	0.83[EUR][1000 genomes]
rs7647905	0.89[EUR][1000 genomes]
rs7648883	0.81[EUR][1000 genomes]
rs7652792	0.88[EUR][1000 genomes]
rs767685	0.88[EUR][1000 genomes]
rs9310516	0.85[EUR][1000 genomes]
rs9631485	0.82[ASN][1000 genomes]
rs9813532	0.87[EUR][1000 genomes]
rs9817290	0.91[EUR][1000 genomes]
rs9820703	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9824952	0.87[EUR][1000 genomes]
rs9830240	0.92[EUR][1000 genomes]
rs9843640	0.88[EUR][1000 genomes]
rs9848766	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9850127	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9851518	0.87[EUR][1000 genomes]
rs9858820	0.82[ASN][1000 genomes]
rs9861749	0.81[EUR][1000 genomes]
rs9864494	0.87[EUR][1000 genomes]
rs9874826	0.87[EUR][1000 genomes]
rs9882273	0.87[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	nsv589841	chr3:17214070-17290465	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv876588	chr3:17214070-17314872	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv876589	chr3:17230884-17346355	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv876590	chr3:17230884-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2755406	chr3:17237396-17589896	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3384458	chr3:17272086-17272431	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17221600-17295800	Weak transcription	HSMM	muscle
2	chr3:17244200-17280600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:17244600-17274600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:17244600-17279400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:17244600-17280600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:17244600-17282000	Weak transcription	Gastric	stomach
7	chr3:17244600-17282800	Weak transcription	Pancreas	Pancrea
8	chr3:17244800-17280400	Weak transcription	Fetal Stomach	stomach
9	chr3:17245800-17281200	Weak transcription	Lung	lung
10	chr3:17250000-17330200	Weak transcription	Aorta	Aorta
11	chr3:17254800-17273200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:17254800-17279600	Weak transcription	Ovary	ovary
13	chr3:17255000-17274800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:17255000-17297000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:17255200-17278600	Weak transcription	Liver	Liver
16	chr3:17255200-17281000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:17255200-17363800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:17262000-17278600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr3:17263200-17274800	Weak transcription	Primary T cells from cord blood	blood
20	chr3:17263200-17274800	Weak transcription	Dnd41	blood
21	chr3:17263200-17279200	Weak transcription	Left Ventricle	heart
22	chr3:17263200-17307200	Weak transcription	Fetal Intestine Small	intestine
23	chr3:17263400-17275800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:17264200-17275800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:17265200-17274800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:17267200-17278800	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:17267800-17273200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:17268800-17273000	Weak transcription	Primary B cells from cord blood	blood
29	chr3:17269800-17278800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:17270000-17273000	Weak transcription	GM12878-XiMat	blood
31	chr3:17271000-17279000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:17271600-17273200	Weak transcription	Fetal Heart	heart

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