Variant report

Variant	rs513977
Chromosome Location	chr1:78616594-78616595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs11162418	0.82[ASN][1000 genomes]
rs11162420	0.82[ASN][1000 genomes]
rs11162421	0.82[ASN][1000 genomes]
rs11162422	0.82[ASN][1000 genomes]
rs11162423	0.80[ASN][1000 genomes]
rs11584032	0.82[ASN][1000 genomes]
rs12082228	0.81[ASN][1000 genomes]
rs12083265	0.82[ASN][1000 genomes]
rs12131414	0.82[ASN][1000 genomes]
rs12133075	0.85[ASN][1000 genomes]
rs12749252	0.82[ASN][1000 genomes]
rs1359043	0.82[ASN][1000 genomes]
rs1407747	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1407748	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1510245	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1621088	0.82[ASN][1000 genomes]
rs1625234	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1770306	0.81[ASN][1000 genomes]
rs1770307	0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2025610	0.82[ASN][1000 genomes]
rs2025611	0.82[ASN][1000 genomes]
rs2025612	0.86[ASN][1000 genomes]
rs2025613	0.85[ASN][1000 genomes]
rs2025614	0.86[ASN][1000 genomes]
rs2209472	0.82[ASN][1000 genomes]
rs2351907	0.82[ASN][1000 genomes]
rs2351909	0.82[ASN][1000 genomes]
rs2351910	0.82[ASN][1000 genomes]
rs2882796	0.80[ASN][1000 genomes]
rs2882797	0.80[ASN][1000 genomes]
rs2882798	0.82[ASN][1000 genomes]
rs4258183	0.82[ASN][1000 genomes]
rs4258184	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4268312	0.82[ASN][1000 genomes]
rs4285658	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4396076	0.83[ASN][1000 genomes]
rs4529663	0.82[ASN][1000 genomes]
rs4587522	0.82[ASN][1000 genomes]
rs4650313	0.82[ASN][1000 genomes]
rs4650315	0.82[ASN][1000 genomes]
rs4650607	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs488469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494496	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs501774	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507045	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs513245	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521029	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs522952	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs523751	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs524031	0.89[CEU][hapmap]
rs524757	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs526723	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs531841	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs534283	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs540742	1.00[CEU][hapmap]
rs554298	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs556170	1.00[CEU][hapmap]
rs557688	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs558643	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561289	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561300	0.81[AMR][1000 genomes]
rs566236	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs577978	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs580426	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582281	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582395	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582795	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs584660	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585072	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs585100	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58611517	0.82[ASN][1000 genomes]
rs586333	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs587433	1.00[CEU][hapmap]
rs591343	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs593652	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs595384	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs597063	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs597272	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs599386	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs599417	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs599730	1.00[CEU][hapmap]
rs600781	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs605659	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60588097	0.81[ASN][1000 genomes]
rs609359	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs609390	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610508	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs612486	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs614836	0.91[AMR][1000 genomes]
rs614963	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs617195	1.00[CEU][hapmap]
rs618063	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs618551	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618581	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs618593	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624766	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627493	0.81[ASN][1000 genomes]
rs627549	0.81[ASN][1000 genomes]
rs627654	1.00[CEU][hapmap]
rs627661	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs629947	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633227	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633664	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs633769	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs634741	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs637943	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642248	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6424716	0.82[ASN][1000 genomes]
rs6424717	0.82[ASN][1000 genomes]
rs644332	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs644359	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs647809	0.86[AFR][1000 genomes]
rs649502	0.81[ASN][1000 genomes]
rs650495	0.82[AMR][1000 genomes]
rs651413	0.84[AMR][1000 genomes]
rs651897	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs656372	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659902	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs661844	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs663254	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs672391	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674933	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs675799	0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs677875	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs680971	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs683097	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs684657	0.87[ASN][1000 genomes]
rs684996	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs685393	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs685848	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs687708	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs699009	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7367729	0.81[ASN][1000 genomes]
rs7367884	0.90[ASN][1000 genomes]
rs7417073	0.82[ASN][1000 genomes]
rs7515450	0.90[ASN][1000 genomes]
rs7518152	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7532752	0.82[ASN][1000 genomes]
rs7555504	0.82[ASN][1000 genomes]
rs812097	0.94[CEU][hapmap]
rs9425188	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs513977	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78584200-78630600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:78609000-78618000	Weak transcription	Colonic Mucosa	Colon
3	chr1:78609200-78624600	Weak transcription	Pancreas	Pancrea
4	chr1:78609200-78624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:78609400-78619000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:78609600-78620800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:78611600-78631400	Weak transcription	Liver	Liver
8	chr1:78613000-78619000	Weak transcription	Duodenum Mucosa	Duodenum

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