Variant report

Variant	rs12999474
Chromosome Location	chr2:186978502-186978503
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 211 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:201)

rs_ID	r²[population]
rs10153530	0.89[ASN][1000 genomes]
rs10165461	0.92[ASN][1000 genomes]
rs10172564	0.92[ASN][1000 genomes]
rs10173075	0.81[ASN][1000 genomes]
rs10174177	0.92[ASN][1000 genomes]
rs10175720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10175815	0.85[ASN][1000 genomes]
rs10177182	0.96[ASN][1000 genomes]
rs10181229	0.96[ASN][1000 genomes]
rs10184559	0.92[ASN][1000 genomes]
rs10186061	0.80[ASN][1000 genomes]
rs10186776	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs10186974	0.81[ASN][1000 genomes]
rs10187040	0.95[ASN][1000 genomes]
rs10189482	0.96[ASN][1000 genomes]
rs10189763	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10189831	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10189845	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10189985	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10190713	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10193227	0.89[ASN][1000 genomes]
rs10193729	0.86[JPT][hapmap]
rs10194241	0.81[ASN][1000 genomes]
rs10196449	0.81[ASN][1000 genomes]
rs10197403	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10200077	0.96[ASN][1000 genomes]
rs10200354	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10202553	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10205061	0.97[ASN][1000 genomes]
rs10205148	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10205245	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10205253	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10497667	0.82[ASN][1000 genomes]
rs10931218	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10931222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931223	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10931228	0.80[ASN][1000 genomes]
rs12233006	0.80[ASN][1000 genomes]
rs12327903	0.89[ASN][1000 genomes]
rs12327910	0.89[ASN][1000 genomes]
rs12328007	0.96[ASN][1000 genomes]
rs12328015	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12373738	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12373744	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12614513	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614595	0.82[ASN][1000 genomes]
rs12615692	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615770	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12615895	0.82[ASN][1000 genomes]
rs12616722	0.81[ASN][1000 genomes]
rs12617754	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621910	0.92[ASN][1000 genomes]
rs12622503	0.92[ASN][1000 genomes]
rs12693431	0.96[ASN][1000 genomes]
rs12693432	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12693434	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12693436	0.95[ASN][1000 genomes]
rs12693437	0.96[ASN][1000 genomes]
rs12988403	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12990062	0.92[ASN][1000 genomes]
rs12994334	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12994860	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12998383	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12999989	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13003934	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13005466	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13014905	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13019653	0.96[ASN][1000 genomes]
rs13022305	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13028175	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13383010	0.96[ASN][1000 genomes]
rs13383401	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13388196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13389991	0.89[ASN][1000 genomes]
rs13394129	0.91[ASN][1000 genomes]
rs13399174	0.81[ASN][1000 genomes]
rs13403908	0.96[ASN][1000 genomes]
rs13407103	0.92[ASN][1000 genomes]
rs13416226	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13417379	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13419562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13420379	0.86[JPT][hapmap]
rs13421172	0.89[ASN][1000 genomes]
rs13422495	0.96[ASN][1000 genomes]
rs13424906	0.81[ASN][1000 genomes]
rs13425057	0.81[ASN][1000 genomes]
rs13429238	0.89[ASN][1000 genomes]
rs13429778	0.96[ASN][1000 genomes]
rs1386516	0.96[ASN][1000 genomes]
rs1386517	0.96[ASN][1000 genomes]
rs1386523	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16827461	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16827480	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16827536	0.81[ASN][1000 genomes]
rs16827550	0.81[ASN][1000 genomes]
rs16827554	0.81[ASN][1000 genomes]
rs16827557	0.81[ASN][1000 genomes]
rs16827559	0.81[ASN][1000 genomes]
rs16827564	0.81[ASN][1000 genomes]
rs16827586	0.81[ASN][1000 genomes]
rs16827599	0.81[ASN][1000 genomes]
rs16827602	0.81[ASN][1000 genomes]
rs2029232	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2029233	0.92[ASN][1000 genomes]
rs2370660	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2370661	0.87[JPT][hapmap]
rs2370670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2370671	0.81[ASN][1000 genomes]
rs2370672	0.81[ASN][1000 genomes]
rs2370674	0.81[ASN][1000 genomes]
rs2370676	0.81[ASN][1000 genomes]
rs2370677	0.83[ASN][1000 genomes]
rs2370679	0.81[ASN][1000 genomes]
rs2370680	0.81[ASN][1000 genomes]
rs2370681	0.80[ASN][1000 genomes]
rs2887769	0.92[ASN][1000 genomes]
rs2887816	0.81[ASN][1000 genomes]
rs34064534	0.96[ASN][1000 genomes]
rs34078354	0.96[ASN][1000 genomes]
rs34113619	0.83[ASN][1000 genomes]
rs34133588	0.83[ASN][1000 genomes]
rs34176985	0.82[ASN][1000 genomes]
rs34612138	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34651427	0.81[ASN][1000 genomes]
rs34749517	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34750486	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34753519	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34916921	0.96[ASN][1000 genomes]
rs35141795	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35156447	0.81[ASN][1000 genomes]
rs35252434	0.83[ASN][1000 genomes]
rs35298515	0.82[ASN][1000 genomes]
rs35504474	0.81[ASN][1000 genomes]
rs35511463	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35522677	0.82[ASN][1000 genomes]
rs35567611	0.81[ASN][1000 genomes]
rs35590244	0.82[ASN][1000 genomes]
rs35652084	0.89[ASN][1000 genomes]
rs35709645	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35811272	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35860748	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35942256	0.83[ASN][1000 genomes]
rs4130833	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4130834	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4264536	0.99[ASN][1000 genomes]
rs4284795	0.82[ASN][1000 genomes]
rs4338930	0.88[ASN][1000 genomes]
rs4381751	0.92[ASN][1000 genomes]
rs4386289	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4417686	0.89[ASN][1000 genomes]
rs4420679	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4442964	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4461230	0.81[ASN][1000 genomes]
rs4471852	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4493221	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4494701	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4552153	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4591311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4591314	0.89[ASN][1000 genomes]
rs4600605	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4614896	0.83[ASN][1000 genomes]
rs4643502	0.81[ASN][1000 genomes]
rs55690692	0.92[ASN][1000 genomes]
rs56309229	0.97[ASN][1000 genomes]
rs57423042	0.96[ASN][1000 genomes]
rs58489224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59252797	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60344273	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60534107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60746023	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61558722	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61573398	0.91[ASN][1000 genomes]
rs62199045	0.96[ASN][1000 genomes]
rs66610853	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66646464	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713702	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6715226	0.91[JPT][hapmap]
rs6725624	0.99[ASN][1000 genomes]
rs6750636	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67872787	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72893941	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72893980	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72893984	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72899807	0.99[ASN][1000 genomes]
rs72899827	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72901780	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72903616	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72903625	0.92[ASN][1000 genomes]
rs72903626	0.92[ASN][1000 genomes]
rs72903630	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72903638	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72905629	0.81[ASN][1000 genomes]
rs7559953	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7582258	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584724	0.81[ASN][1000 genomes]
rs8179713	0.82[ASN][1000 genomes]
rs875162	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9288123	0.92[ASN][1000 genomes]
rs9288124	0.89[ASN][1000 genomes]
rs9630989	0.95[ASN][1000 genomes]
rs991084	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv817325	chr2:186625679-187200841	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1002243	chr2:186692815-187150225	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv536077	chr2:186692815-187150225	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv875547	chr2:186798249-187014815	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv875548	chr2:186798249-187164657	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv584030	chr2:186915437-187001076	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3329676	chr2:186972495-186994906	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186966200-186980800	Weak transcription	Small Intestine	intestine
2	chr2:186970400-186981400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:186977800-186979600	Weak transcription	Left Ventricle	heart
4	chr2:186978000-186984400	Weak transcription	Ovary	ovary
5	chr2:186978200-186981000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:186978200-186989400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:186978400-186979000	Weak transcription	Pancreas	Pancrea
8	chr2:186978400-186990800	Weak transcription	Psoas Muscle	Psoas

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