Variant report

Variant	rs659902
Chromosome Location	chr1:78645636-78645637
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs11162418	0.85[ASN][1000 genomes]
rs11162420	0.83[ASN][1000 genomes]
rs11162421	0.85[ASN][1000 genomes]
rs11162422	0.83[ASN][1000 genomes]
rs11162423	0.83[ASN][1000 genomes]
rs11584032	0.85[ASN][1000 genomes]
rs12082228	0.84[ASN][1000 genomes]
rs12083265	0.85[ASN][1000 genomes]
rs12131414	0.85[ASN][1000 genomes]
rs12133075	0.80[ASN][1000 genomes]
rs12749252	0.85[ASN][1000 genomes]
rs1359043	0.85[ASN][1000 genomes]
rs1407747	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1407748	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1621088	0.85[ASN][1000 genomes]
rs1625234	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1770306	0.86[ASN][1000 genomes]
rs1770307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025610	0.85[ASN][1000 genomes]
rs2025611	0.85[ASN][1000 genomes]
rs2025612	0.81[ASN][1000 genomes]
rs2025613	0.80[ASN][1000 genomes]
rs2025614	0.81[ASN][1000 genomes]
rs2209472	0.85[ASN][1000 genomes]
rs2351907	0.85[ASN][1000 genomes]
rs2351909	0.85[ASN][1000 genomes]
rs2351910	0.85[ASN][1000 genomes]
rs2882796	0.83[ASN][1000 genomes]
rs2882797	0.83[ASN][1000 genomes]
rs2882798	0.85[ASN][1000 genomes]
rs4258183	0.85[ASN][1000 genomes]
rs4258184	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4268312	0.85[ASN][1000 genomes]
rs4285658	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4396076	0.84[ASN][1000 genomes]
rs4529663	0.85[ASN][1000 genomes]
rs4587522	0.85[ASN][1000 genomes]
rs4650313	0.85[ASN][1000 genomes]
rs4650315	0.85[ASN][1000 genomes]
rs4650607	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs488469	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs494496	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs501774	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs513245	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs513977	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs521029	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs523751	0.88[ASN][1000 genomes]
rs526723	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs531841	0.86[ASN][1000 genomes]
rs554298	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs557688	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs558643	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs561289	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs577978	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs580426	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs581926	0.84[ASN][1000 genomes]
rs582281	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs582395	0.88[ASN][1000 genomes]
rs582795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584660	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs585100	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58611517	0.85[ASN][1000 genomes]
rs591343	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593652	0.87[ASN][1000 genomes]
rs597063	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597272	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599386	0.89[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs600781	0.88[ASN][1000 genomes]
rs605659	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs609359	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs609390	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs610508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612486	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs614836	0.87[AMR][1000 genomes]
rs614963	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61777350	0.84[ASN][1000 genomes]
rs618063	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618551	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs618581	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs618593	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs624766	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs627493	0.86[ASN][1000 genomes]
rs627549	0.86[ASN][1000 genomes]
rs627661	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs629947	0.88[ASN][1000 genomes]
rs633227	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs633664	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs633769	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs634741	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs637943	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs642248	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6424716	0.85[ASN][1000 genomes]
rs6424717	0.85[ASN][1000 genomes]
rs644332	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs644359	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs647809	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs648315	0.84[AMR][1000 genomes]
rs649502	0.86[ASN][1000 genomes]
rs656372	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs658212	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs663254	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6665090	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs672391	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs674933	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs675799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677875	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs680143	0.84[ASN][1000 genomes]
rs680971	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683097	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs684657	0.82[ASN][1000 genomes]
rs684996	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs687708	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs688570	0.80[ASN][1000 genomes]
rs699009	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7367729	0.82[ASN][1000 genomes]
rs7367884	0.88[ASN][1000 genomes]
rs7417073	0.85[ASN][1000 genomes]
rs7515450	0.88[ASN][1000 genomes]
rs7518152	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7532752	0.85[ASN][1000 genomes]
rs7555504	0.85[ASN][1000 genomes]
rs9425188	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1000388	chr1:78638946-78665285	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv520237	chr1:78639244-78660123	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs659902	NEXN	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78635000-78646200	Weak transcription	Fetal Intestine Small	intestine

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