Variant report

Variant	rs2065922
Chromosome Location	chr1:103494942-103494943
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 181 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs1012282	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10458505	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10493988	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10493991	1.00[JPT][hapmap]
rs10747437	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782918	0.82[AFR][1000 genomes]
rs10782921	0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap]
rs10874665	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10874668	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10874677	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874678	0.84[ASN][1000 genomes]
rs10874679	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11164648	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11164649	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164650	0.88[ASN][1000 genomes]
rs11164653	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11164657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164658	0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs11164662	0.86[ASN][1000 genomes]
rs11164665	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11164668	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11164669	0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11164672	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11809524	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11811018	1.00[JPT][hapmap]
rs12025848	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12036215	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042830	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043105	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12047268	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12092111	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12118365	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12119459	1.00[JPT][hapmap]
rs12123031	1.00[JPT][hapmap]
rs12124588	1.00[JPT][hapmap]
rs12127590	1.00[JPT][hapmap]
rs12136338	0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs12136748	1.00[JPT][hapmap]
rs12139120	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12142575	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1241162	1.00[JPT][hapmap]
rs1241166	1.00[JPT][hapmap]
rs1241181	1.00[JPT][hapmap]
rs1241182	1.00[JPT][hapmap]
rs1241183	1.00[JPT][hapmap]
rs12717796	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
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	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12731843	1.00[JPT][hapmap]
rs12733933	1.00[JPT][hapmap]
rs12738133	1.00[JPT][hapmap]
rs12740738	0.86[ASN][1000 genomes]
rs12743365	1.00[JPT][hapmap]
rs12744290	1.00[JPT][hapmap]
rs12744488	1.00[JPT][hapmap]
rs12750377	1.00[JPT][hapmap]
rs12755987	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12756627	1.00[JPT][hapmap]
rs1337174	1.00[JPT][hapmap]
rs1337175	1.00[JPT][hapmap]
rs1337186	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1337191	0.84[ASN][1000 genomes]
rs1415359	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1415361	0.84[ASN][1000 genomes]
rs1415364	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1463034	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1463035	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1463037	1.00[JPT][hapmap]
rs1463038	1.00[JPT][hapmap]
rs1463039	1.00[JPT][hapmap]
rs1538041	0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs1564143	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1564144	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1572515	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1591636	0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap]
rs1591637	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1621055	1.00[JPT][hapmap]
rs1622838	1.00[JPT][hapmap]
rs1676493	1.00[JPT][hapmap]
rs1676494	1.00[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]
rs1824691	0.88[ASN][1000 genomes]
rs1870958	1.00[JPT][hapmap]
rs1903787	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1966959	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2050601	0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.82[AFR][1000 genomes]
rs2061704	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2252146	1.00[JPT][hapmap]
rs2254082	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2376280	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2376281	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2615977	0.89[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2615987	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2615999	1.00[JPT][hapmap]
rs2622844	0.84[ASN][1000 genomes]
rs2622846	0.88[ASN][1000 genomes]
rs2622848	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622854	0.88[ASN][1000 genomes]
rs2622870	1.00[JPT][hapmap]
rs2622873	0.92[ASN][1000 genomes]
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	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2786121	1.00[JPT][hapmap]
rs2786122	1.00[JPT][hapmap]
rs2786125	1.00[JPT][hapmap]
rs2889351	0.86[ASN][1000 genomes]
rs2929163	1.00[JPT][hapmap]
rs3102053	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34765476	0.91[CHD][hapmap]
rs3767272	0.82[JPT][hapmap]
rs3850459	1.00[JPT][hapmap]
rs3908854	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4098282	0.92[ASN][1000 genomes]
rs4338381	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4391683	0.84[ASN][1000 genomes]
rs4478834	0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs4907986	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4908280	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4908281	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4908283	0.81[AFR][1000 genomes]
rs4908286	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4908291	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6663034	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6670486	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6672647	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6695665	0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap]
rs6699118	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7517682	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7532572	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544130	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7550118	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7552614	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs945748	0.89[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986944	0.88[ASN][1000 genomes]
rs9970114	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv870600	chr1:103336601-103548497	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871475	chr1:103339272-103548497	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv871741	chr1:103352451-103517428	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv871078	chr1:103352451-103548497	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv870607	chr1:103362909-103528128	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv870995	chr1:103384610-103548497	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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
9	nsv871067	chr1:103407999-103509323	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv871736	chr1:103409100-103548497	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv871567	chr1:103416690-103499049	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv871657	chr1:103427381-103528128	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv871198	chr1:103432687-103498029	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv546935	chr1:103438795-103498029	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv462772	chr1:103438795-103499896	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv546936	chr1:103438795-103499896	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv462783	chr1:103438795-103548497	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv546937	chr1:103438795-103548497	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv462794	chr1:103450196-103539007	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv546938	chr1:103450196-103539007	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv871286	chr1:103455217-103528128	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	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
23	nsv871733	chr1:103459537-103509323	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv871071	chr1:103471962-103509323	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv871365	chr1:103476179-103548497	Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	esv1835970	chr1:103481299-103510756	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2065922	DBT	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103369600-103498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:103446800-103497800	Weak transcription	HSMM	muscle
3	chr1:103449200-103545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:103460200-103516400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:103475800-103516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:103489200-103516400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:103489600-103506000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:103491600-103503800	Weak transcription	NH-A	brain
9	chr1:103492000-103496400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:103492400-103497200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:103493800-103495600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:103494000-103500200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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