Variant report

Variant	rs2025611
Chromosome Location	chr1:78623973-78623974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10873966	0.85[EUR][1000 genomes]
rs11162418	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162420	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162421	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162422	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11162423	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162425	0.85[EUR][1000 genomes]
rs11584032	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082228	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12083265	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095545	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12131414	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133075	0.95[ASN][1000 genomes]
rs12749252	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323094	0.85[EUR][1000 genomes]
rs1359043	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407747	0.86[ASN][1000 genomes]
rs1407748	0.86[ASN][1000 genomes]
rs1621088	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625234	0.86[ASN][1000 genomes]
rs1770306	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1770307	0.85[ASN][1000 genomes]
rs2025610	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025612	0.96[ASN][1000 genomes]
rs2025613	0.95[ASN][1000 genomes]
rs2025614	0.96[ASN][1000 genomes]
rs2146612	0.85[EUR][1000 genomes]
rs2208966	0.85[EUR][1000 genomes]
rs2209472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209473	0.86[AMR][1000 genomes]
rs2351907	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351909	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351910	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882796	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2882797	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2882798	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258183	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258184	0.86[ASN][1000 genomes]
rs4268312	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285658	0.86[ASN][1000 genomes]
rs4396076	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4529663	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587522	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650313	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650315	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650607	0.84[ASN][1000 genomes]
rs488469	0.82[ASN][1000 genomes]
rs501774	0.82[ASN][1000 genomes]
rs513245	0.82[ASN][1000 genomes]
rs513977	0.82[ASN][1000 genomes]
rs561289	0.82[ASN][1000 genomes]
rs581926	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582795	0.85[ASN][1000 genomes]
rs58611517	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591343	0.83[ASN][1000 genomes]
rs596803	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597063	0.83[ASN][1000 genomes]
rs597272	0.85[ASN][1000 genomes]
rs599386	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600237	0.80[EUR][1000 genomes]
rs60588097	0.91[ASN][1000 genomes]
rs610508	0.85[ASN][1000 genomes]
rs616518	0.82[EUR][1000 genomes]
rs61777350	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs618063	0.81[ASN][1000 genomes]
rs618551	0.82[ASN][1000 genomes]
rs618593	0.82[ASN][1000 genomes]
rs619749	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624766	0.82[ASN][1000 genomes]
rs627493	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627549	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs633664	0.81[ASN][1000 genomes]
rs634741	0.85[ASN][1000 genomes]
rs637943	0.82[ASN][1000 genomes]
rs640124	0.85[EUR][1000 genomes]
rs6424716	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424717	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644332	0.84[ASN][1000 genomes]
rs649502	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs651413	0.88[ASN][1000 genomes]
rs653899	0.82[EUR][1000 genomes]
rs656372	0.82[ASN][1000 genomes]
rs658212	0.82[ASN][1000 genomes]
rs659902	0.85[ASN][1000 genomes]
rs671229	0.80[EUR][1000 genomes]
rs672391	0.82[ASN][1000 genomes]
rs675799	0.86[ASN][1000 genomes]
rs677875	0.83[ASN][1000 genomes]
rs680143	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs680971	0.83[ASN][1000 genomes]
rs683097	0.82[ASN][1000 genomes]
rs684657	0.95[ASN][1000 genomes]
rs684996	0.83[ASN][1000 genomes]
rs688570	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs689374	0.85[EUR][1000 genomes]
rs699009	0.82[ASN][1000 genomes]
rs72688712	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7367729	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7417073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532752	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555504	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425188	0.85[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
rs2025611	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 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	chr1:78622600-78624000	Enhancers	Osteobl	bone
12	chr1:78623600-78634000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links