Variant report

Variant	rs11164665
Chromosome Location	chr1:103551918-103551919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1012282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10493988	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[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	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164648	1.00[CHB][hapmap];0.87[CHD][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	0.82[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164666	0.88[EUR][1000 genomes]
rs11164667	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164672	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118365	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12119459	1.00[JPT][hapmap]
rs12123031	1.00[JPT][hapmap]
rs12124588	1.00[JPT][hapmap]
rs12127590	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12136338	1.00[JPT][hapmap]
rs12136748	1.00[JPT][hapmap]
rs12139120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142575	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1241162	1.00[JPT][hapmap]
rs1241166	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	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];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	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415359	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415361	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[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	0.88[CEU][hapmap];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	0.88[CHD][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2376281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[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]
rs2783570	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	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];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	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3908854	0.84[ASN][1000 genomes]
rs4338381	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4391683	0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478834	1.00[JPT][hapmap]
rs4907986	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4908280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4908287	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs4908288	0.84[CEU][hapmap]
rs4908289	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4908290	0.87[ASW][hapmap];0.84[CEU][hapmap];0.91[MEX][hapmap];0.87[AMR][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]
rs7517682	0.84[CEU][hapmap];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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9970114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11164665	DBT	cis	cerebellum	SCAN
rs11164665	SNORD116-25	trans	cerebellum	SCAN

Chromatin state (count:8 , 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	chr1:103522400-103559000	Weak transcription	HSMM	muscle
3	chr1:103539600-103556600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:103544000-103570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:103545000-103566800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:103546200-103556000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:103548000-103564400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:103551400-103552000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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