Variant report

Variant	rs513245
Chromosome Location	chr1:78608697-78608698
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

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	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1407748	0.90[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	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1770306	0.81[ASN][1000 genomes]
rs1770307	0.90[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	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4268312	0.82[ASN][1000 genomes]
rs4285658	0.90[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	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs488469	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494496	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs501774	0.98[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]
rs513977	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521029	0.95[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	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs524757	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs526723	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs531841	0.85[AFR][1000 genomes];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]
rs554298	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs557688	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs558643	1.00[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	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs580426	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582281	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582395	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582795	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs584660	0.97[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	0.97[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]
rs591343	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs593652	0.89[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	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs597272	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs599386	0.82[ASN][1000 genomes]
rs599417	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs600781	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs605659	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60588097	0.81[ASN][1000 genomes]
rs609359	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs609390	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610508	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs612486	0.97[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	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs618063	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs618551	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618581	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs618593	1.00[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]
rs627661	0.85[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	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633664	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs633769	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs634741	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs637943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642248	0.94[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	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs644359	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649502	0.81[ASN][1000 genomes]
rs650495	0.82[AMR][1000 genomes]
rs651413	0.84[AMR][1000 genomes]
rs651897	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs656372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658212	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659902	0.89[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	0.85[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	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs675799	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs677875	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs680971	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs683097	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs684657	0.87[ASN][1000 genomes]
rs684996	0.88[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	0.85[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	0.97[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]
rs9425188	0.88[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
rs513245	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 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	chr1:78603200-78609000	Weak transcription	Fetal Stomach	stomach
3	chr1:78607200-78609600	Enhancers	Fetal Intestine Large	intestine
4	chr1:78607200-78609600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:78607200-78609800	Enhancers	Small Intestine	intestine
6	chr1:78607600-78609200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:78608400-78608800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:78608400-78608800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:78608400-78608800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:78608400-78609400	Genic enhancers	Fetal Intestine Small	intestine
11	chr1:78608400-78609600	Flanking Active TSS	GM12878-XiMat	blood
12	chr1:78608600-78608800	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:78608600-78608800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:78608600-78608800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:78608600-78608800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:78608600-78608800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr1:78608600-78608800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:78608600-78608800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:78608600-78608800	Genic enhancers	Pancreas	Pancrea
20	chr1:78608600-78608800	Enhancers	Psoas Muscle	Psoas
21	chr1:78608600-78608800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:78608600-78608800	Enhancers	Thymus	Thymus
23	chr1:78608600-78608800	Enhancers	Dnd41	blood
24	chr1:78608600-78609000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr1:78608600-78609000	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr1:78608600-78609000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:78608600-78609000	Enhancers	Colonic Mucosa	Colon
28	chr1:78608600-78609200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:78608600-78609200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:78608600-78609200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:78608600-78609200	Flanking Active TSS	Liver	Liver
32	chr1:78608600-78609400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr1:78608600-78609400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:78608600-78609400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:78608600-78609400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr1:78608600-78610200	Enhancers	HepG2	liver

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