Variant report

Variant	rs12142575
Chromosome Location	chr1:103558163-103558164
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1012282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10493986	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs10493988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493991	1.00[JPT][hapmap]
rs10747437	0.96[ASN][1000 genomes]
rs10782921	1.00[JPT][hapmap]
rs10874665	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10874668	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10874677	0.96[ASN][1000 genomes]
rs10874678	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874679	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164649	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164657	0.84[ASN][1000 genomes]
rs11164658	1.00[JPT][hapmap]
rs11164662	0.88[CHB][hapmap];0.98[ASN][1000 genomes]
rs11164665	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164668	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164669	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586849	0.83[CEU][hapmap]
rs11809524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11811018	1.00[JPT][hapmap]
rs12025848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12036215	0.84[ASN][1000 genomes]
rs12042830	0.80[ASN][1000 genomes]
rs12047268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12092111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12119459	1.00[JPT][hapmap]
rs12123031	1.00[JPT][hapmap]
rs12124588	1.00[JPT][hapmap]
rs12127590	1.00[JPT][hapmap]
rs12136338	1.00[JPT][hapmap]
rs12136748	1.00[JPT][hapmap]
rs12139120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12723167	1.00[JPT][hapmap]
rs12723922	1.00[JPT][hapmap]
rs12724152	1.00[JPT][hapmap]
rs12726958	1.00[JPT][hapmap]
rs12727959	1.00[JPT][hapmap]
rs12728397	1.00[JPT][hapmap]
rs12729449	1.00[JPT][hapmap]
rs12729602	1.00[JPT][hapmap]
rs12731843	1.00[JPT][hapmap]
rs12733933	1.00[JPT][hapmap]
rs12738133	1.00[JPT][hapmap]
rs12740738	0.98[ASN][1000 genomes]
rs12743365	1.00[JPT][hapmap]
rs12744290	1.00[JPT][hapmap]
rs12744488	1.00[JPT][hapmap]
rs12750377	1.00[JPT][hapmap]
rs12756627	1.00[JPT][hapmap]
rs1337174	1.00[JPT][hapmap]
rs1337175	1.00[JPT][hapmap]
rs1337186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1337191	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337195	0.83[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1415359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415361	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415364	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463034	1.00[JPT][hapmap]
rs1463035	1.00[JPT][hapmap]
rs1463037	1.00[JPT][hapmap]
rs1463038	1.00[JPT][hapmap]
rs1463039	1.00[JPT][hapmap]
rs1538041	1.00[JPT][hapmap]
rs1564143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1591636	1.00[JPT][hapmap]
rs1591637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1621055	1.00[JPT][hapmap]
rs1622838	1.00[JPT][hapmap]
rs1676493	1.00[JPT][hapmap]
rs1676494	0.82[JPT][hapmap]
rs1676497	1.00[JPT][hapmap]
rs1676498	1.00[JPT][hapmap]
rs1676499	1.00[JPT][hapmap]
rs1676500	1.00[JPT][hapmap]
rs1676501	1.00[JPT][hapmap]
rs1676502	1.00[JPT][hapmap]
rs17506286	1.00[JPT][hapmap]
rs17507967	1.00[JPT][hapmap]
rs1763344	1.00[JPT][hapmap]
rs1763345	1.00[JPT][hapmap]
rs1763346	1.00[JPT][hapmap]
rs1870958	1.00[JPT][hapmap]
rs1903787	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2050601	1.00[JPT][hapmap]
rs2061704	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2065922	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2252146	1.00[JPT][hapmap]
rs2254082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2376280	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2376281	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615977	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2615987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2622848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2622870	1.00[JPT][hapmap]
rs2622874	1.00[JPT][hapmap]
rs2622876	1.00[JPT][hapmap]
rs2622877	1.00[JPT][hapmap]
rs2622880	1.00[JPT][hapmap]
rs2786120	1.00[JPT][hapmap]
rs2786121	1.00[JPT][hapmap]
rs2786122	1.00[JPT][hapmap]
rs2786125	1.00[JPT][hapmap]
rs2889351	0.98[ASN][1000 genomes]
rs2929163	1.00[JPT][hapmap]
rs3102053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3767272	0.82[JPT][hapmap]
rs3850459	1.00[JPT][hapmap]
rs3908854	0.84[ASN][1000 genomes]
rs4338381	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4391683	1.00[ASN][1000 genomes]
rs4478834	1.00[JPT][hapmap]
rs4907986	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4908280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908286	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4908289	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4908291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6663034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6670486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6672647	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6695665	1.00[JPT][hapmap]
rs7416903	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7517682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7532572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7544130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7550118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9970114	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103522400-103559000	Weak transcription	HSMM	muscle
2	chr1:103544000-103570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:103545000-103566800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:103548000-103564400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:103556400-103559200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:103558000-103558400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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