Variant report

Variant	rs1407747
Chromosome Location	chr1:78623330-78623331
allele	A/G
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:124)

rs_ID	r²[population]
rs11162418	0.86[ASN][1000 genomes]
rs11162420	0.84[ASN][1000 genomes]
rs11162421	0.86[ASN][1000 genomes]
rs11162422	0.84[ASN][1000 genomes]
rs11162423	0.84[ASN][1000 genomes]
rs11162433	0.86[CEU][hapmap]
rs11584032	0.86[ASN][1000 genomes]
rs12082228	0.85[ASN][1000 genomes]
rs12083265	0.86[ASN][1000 genomes]
rs12131414	0.86[ASN][1000 genomes]
rs12133075	0.81[ASN][1000 genomes]
rs12749252	0.86[ASN][1000 genomes]
rs1359043	0.86[ASN][1000 genomes]
rs1407748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621088	0.86[ASN][1000 genomes]
rs1625234	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770306	0.85[ASN][1000 genomes]
rs1770307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2025610	0.86[ASN][1000 genomes]
rs2025611	0.86[ASN][1000 genomes]
rs2025612	0.82[ASN][1000 genomes]
rs2025613	0.81[ASN][1000 genomes]
rs2025614	0.82[ASN][1000 genomes]
rs2209472	0.86[ASN][1000 genomes]
rs2351907	0.86[ASN][1000 genomes]
rs2351909	0.86[ASN][1000 genomes]
rs2351910	0.86[ASN][1000 genomes]
rs2882796	0.84[ASN][1000 genomes]
rs2882797	0.84[ASN][1000 genomes]
rs2882798	0.86[ASN][1000 genomes]
rs4258183	0.86[ASN][1000 genomes]
rs4258184	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268312	0.86[ASN][1000 genomes]
rs4285658	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4396076	0.85[ASN][1000 genomes]
rs4529663	0.86[ASN][1000 genomes]
rs4587522	0.86[ASN][1000 genomes]
rs4650313	0.86[ASN][1000 genomes]
rs4650315	0.86[ASN][1000 genomes]
rs4650607	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs488469	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs494496	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs501774	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs513245	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs513977	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs521029	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs523751	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs524757	0.81[AMR][1000 genomes]
rs526723	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs531841	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs554298	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs557688	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs558643	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs561289	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs577978	0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs580426	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs581926	0.83[ASN][1000 genomes]
rs582281	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs582395	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs582795	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584660	0.94[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs585100	0.94[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58611517	0.86[ASN][1000 genomes]
rs591343	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs593652	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs597063	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs597272	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs599386	0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs600781	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs605659	0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs609359	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs609390	0.87[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs610508	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612486	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs614836	0.93[CEU][hapmap];0.91[AMR][1000 genomes]
rs614963	0.94[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61777350	0.83[ASN][1000 genomes]
rs618063	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs618551	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs618581	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs618593	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs624766	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs627493	0.85[ASN][1000 genomes]
rs627549	0.85[ASN][1000 genomes]
rs627661	0.94[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs629947	0.89[ASN][1000 genomes]
rs633227	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs633664	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs633769	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs634741	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs637943	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs642248	0.94[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6424716	0.86[ASN][1000 genomes]
rs6424717	0.86[ASN][1000 genomes]
rs644332	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs644359	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs647809	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs648315	0.81[AMR][1000 genomes]
rs649502	0.85[ASN][1000 genomes]
rs656372	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs658212	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs659902	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs663254	0.94[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6665090	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs672391	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs674933	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs675799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677875	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs680143	0.83[ASN][1000 genomes]
rs680971	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683097	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684657	0.83[ASN][1000 genomes]
rs684996	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs687708	0.94[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs699009	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7367729	0.83[ASN][1000 genomes]
rs7367884	0.89[ASN][1000 genomes]
rs7417073	0.86[ASN][1000 genomes]
rs7515450	0.89[ASN][1000 genomes]
rs7518152	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7532752	0.86[ASN][1000 genomes]
rs7555504	0.86[ASN][1000 genomes]
rs812097	0.81[CEU][hapmap]
rs9425188	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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
rs1407747	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 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	chr1:78609200-78624600	Weak transcription	Pancreas	Pancrea
3	chr1:78609200-78624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:78611600-78631400	Weak transcription	Liver	Liver
5	chr1:78619800-78624400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:78619800-78624600	Weak transcription	Spleen	Spleen
7	chr1:78620600-78624200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:78621200-78624600	Weak transcription	Fetal Intestine Large	intestine
9	chr1:78621200-78626800	Weak transcription	Right Ventricle	heart
10	chr1:78621400-78625400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:78621800-78623800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:78622000-78623800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:78622000-78623800	Enhancers	Hela-S3	cervix
14	chr1:78622400-78623600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:78622400-78623600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:78622400-78623600	Enhancers	NHLF	lung
17	chr1:78622400-78623800	Enhancers	HMEC	breast
18	chr1:78622600-78623400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:78622600-78623800	Enhancers	NHEK	skin
20	chr1:78622600-78624000	Enhancers	Osteobl	bone
21	chr1:78622800-78623400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:78622800-78623600	Enhancers	Fetal Lung	lung
23	chr1:78622800-78623800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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