Variant report

Variant	rs12727959
Chromosome Location	chr1:103550401-103550402
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	chr1:103546900..103548973-chr1:103549511..103551130,2	K562	blood:

Variant related genes	Relation type
ENSG00000060718	Chromatin interaction

Extended variants
information (count: 269 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:265)

rs_ID	r²[population]
rs1012282	1.00[JPT][hapmap]
rs10493988	1.00[JPT][hapmap]
rs10493991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10735777	0.92[ASN][1000 genomes]
rs10782918	0.87[ASN][1000 genomes]
rs10782921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10874665	1.00[JPT][hapmap]
rs10874668	1.00[JPT][hapmap]
rs10874672	0.82[ASN][1000 genomes]
rs10874679	1.00[JPT][hapmap]
rs11164648	1.00[JPT][hapmap]
rs11164649	1.00[JPT][hapmap]
rs11164653	1.00[JPT][hapmap]
rs11164658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11164665	1.00[JPT][hapmap]
rs11164668	1.00[JPT][hapmap]
rs11164669	0.82[JPT][hapmap]
rs11164672	1.00[JPT][hapmap]
rs11809524	1.00[JPT][hapmap]
rs11811018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12025848	1.00[JPT][hapmap]
rs12047268	1.00[JPT][hapmap]
rs12092111	1.00[JPT][hapmap]
rs12118365	1.00[JPT][hapmap]
rs12119459	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12119661	0.85[ASN][1000 genomes]
rs12121641	0.92[ASN][1000 genomes]
rs12123031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12124588	1.00[JPT][hapmap]
rs12125729	0.87[ASN][1000 genomes]
rs12126622	0.87[ASN][1000 genomes]
rs12127590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12136338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12136748	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12139120	1.00[JPT][hapmap]
rs12142575	1.00[JPT][hapmap]
rs1241162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1241164	1.00[CHB][hapmap]
rs1241166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12722908	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12723167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12723432	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12723922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12724152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12725698	0.87[ASN][1000 genomes]
rs12726009	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs12726958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12727675	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12728397	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12728656	0.87[ASN][1000 genomes]
rs12728737	0.82[ASN][1000 genomes]
rs12728819	0.87[ASN][1000 genomes]
rs12729449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12729588	0.87[ASN][1000 genomes]
rs12729602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12729803	0.87[ASN][1000 genomes]
rs12729964	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12730712	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12731591	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12731843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12733029	0.92[ASN][1000 genomes]
rs12733087	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12733164	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12733249	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12733933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12734491	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12735139	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12737364	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12738118	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12738133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12740092	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12741474	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742130	0.82[ASN][1000 genomes]
rs12742332	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12742440	0.82[ASN][1000 genomes]
rs12742552	0.87[ASN][1000 genomes]
rs12742761	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12743150	0.82[ASN][1000 genomes]
rs12743365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12744290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12744488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12748084	0.89[ASN][1000 genomes]
rs12748384	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12748883	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12749162	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12749361	0.81[ASN][1000 genomes]
rs12749367	0.81[ASN][1000 genomes]
rs12749646	0.87[ASN][1000 genomes]
rs12750147	0.87[ASN][1000 genomes]
rs12750176	0.87[ASN][1000 genomes]
rs12750303	0.87[ASN][1000 genomes]
rs12750377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12750407	0.87[ASN][1000 genomes]
rs12753436	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12753580	0.82[ASN][1000 genomes]
rs12753781	0.82[ASN][1000 genomes]
rs12754215	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12754301	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12754606	0.87[ASN][1000 genomes]
rs12756627	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12757655	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12757965	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1337174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1337175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1337176	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1337177	0.87[ASN][1000 genomes]
rs1337178	0.87[ASN][1000 genomes]
rs1337186	1.00[JPT][hapmap]
rs13374456	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1415359	1.00[JPT][hapmap]
rs1415364	1.00[JPT][hapmap]
rs1463034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1463035	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1463037	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1463038	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1463039	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1538041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1564143	1.00[JPT][hapmap]
rs1591636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1591637	1.00[JPT][hapmap]
rs1621055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1622838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1676493	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1676494	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1676497	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1676498	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1676499	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1676500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1676501	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1676502	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17127510	0.82[EUR][1000 genomes]
rs17447925	1.00[CHB][hapmap]
rs17506286	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17507967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1763344	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1763345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1763346	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1870958	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1903787	1.00[JPT][hapmap]
rs2050601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2061704	1.00[JPT][hapmap]
rs2065922	1.00[JPT][hapmap]
rs2252146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2254082	1.00[JPT][hapmap]
rs2376280	1.00[JPT][hapmap]
rs2376281	1.00[JPT][hapmap]
rs2376284	0.92[ASN][1000 genomes]
rs2615977	1.00[JPT][hapmap]
rs2615987	1.00[JPT][hapmap]
rs2622840	0.82[ASN][1000 genomes]
rs2622848	1.00[JPT][hapmap]
rs2622870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2622874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2622876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2622877	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2622880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2783570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2786120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2786121	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2786122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2786125	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2929163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3102053	1.00[JPT][hapmap]
rs34038518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34110240	0.87[ASN][1000 genomes]
rs34137810	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34138324	0.87[ASN][1000 genomes]
rs34157185	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34206172	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34229612	0.87[ASN][1000 genomes]
rs34243101	0.87[ASN][1000 genomes]
rs34305103	0.87[ASN][1000 genomes]
rs34347324	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34408616	0.87[ASN][1000 genomes]
rs34456893	0.89[ASN][1000 genomes]
rs34587338	0.87[ASN][1000 genomes]
rs34637912	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34727523	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34762213	0.87[ASN][1000 genomes]
rs34765476	0.87[ASN][1000 genomes]
rs34822172	0.97[ASN][1000 genomes]
rs34883734	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34965749	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35037054	0.87[ASN][1000 genomes]
rs35071880	0.87[ASN][1000 genomes]
rs35138059	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35150936	0.82[ASN][1000 genomes]
rs35192078	0.87[ASN][1000 genomes]
rs35196641	0.89[ASN][1000 genomes]
rs35269818	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35278135	0.87[ASN][1000 genomes]
rs35351574	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35384282	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35512814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35514519	0.87[ASN][1000 genomes]
rs35573953	0.92[ASN][1000 genomes]
rs35595325	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35648695	0.87[ASN][1000 genomes]
rs35659176	0.87[ASN][1000 genomes]
rs35671668	0.87[ASN][1000 genomes]
rs35707694	0.87[ASN][1000 genomes]
rs35727167	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35834443	0.89[ASN][1000 genomes]
rs35872185	0.87[ASN][1000 genomes]
rs35884314	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35908252	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35979991	0.87[ASN][1000 genomes]
rs36000197	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36005955	0.87[ASN][1000 genomes]
rs36011373	0.87[ASN][1000 genomes]
rs3767272	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs3850459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3934352	0.82[ASN][1000 genomes]
rs4338381	1.00[JPT][hapmap]
rs4353117	1.00[CHB][hapmap]
rs4478834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4907986	1.00[JPT][hapmap]
rs4908280	1.00[JPT][hapmap]
rs4908283	0.89[ASN][1000 genomes]
rs4908286	1.00[JPT][hapmap]
rs4908291	1.00[JPT][hapmap]
rs56361645	0.82[EUR][1000 genomes]
rs61816501	0.87[ASN][1000 genomes]
rs61816502	0.87[ASN][1000 genomes]
rs61816503	0.87[ASN][1000 genomes]
rs6663034	1.00[JPT][hapmap]
rs6670486	1.00[JPT][hapmap]
rs6672647	1.00[JPT][hapmap]
rs6689957	0.87[ASN][1000 genomes]
rs6695665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs71512568	0.87[ASN][1000 genomes]
rs71592265	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71655803	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71655804	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71655805	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71655806	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71655807	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71655808	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71664952	0.82[ASN][1000 genomes]
rs71664954	0.82[ASN][1000 genomes]
rs71664955	0.82[ASN][1000 genomes]
rs71664959	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71664961	0.87[ASN][1000 genomes]
rs71664962	0.87[ASN][1000 genomes]
rs71664963	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71664964	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71664965	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71664966	0.87[ASN][1000 genomes]
rs71664967	0.87[ASN][1000 genomes]
rs71664968	0.87[ASN][1000 genomes]
rs71664969	0.87[ASN][1000 genomes]
rs71664974	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71664976	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71664978	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71664979	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71664980	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71666999	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517682	1.00[JPT][hapmap]
rs7522293	0.95[ASN][1000 genomes]
rs7532572	1.00[JPT][hapmap]
rs7544130	1.00[JPT][hapmap]
rs7550118	1.00[JPT][hapmap]
rs945748	1.00[JPT][hapmap]
rs951414	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9970114	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv871372	chr1:103403752-103564540	Strong transcription Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv931600	chr1:103548397-104161031	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103517400-103557200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:103517600-103550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:103522400-103559000	Weak transcription	HSMM	muscle
4	chr1:103539600-103556600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:103544000-103570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:103544200-103551800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:103545000-103566800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:103546200-103556000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:103548000-103564400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:103549200-103550600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:103549800-103550600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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