Variant report

Variant	rs58250931
Chromosome Location	chr10:91589226-91589227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr10:91589087-91589282	K562	blood:	n/a	chr10:91589231-91589242 chr10:91589227-91589236 chr10:91589226-91589241 chr10:91589231-91589242

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:91589226-91589276	HCPEpiC	choroid plexus:	n/a
2	chr10:91589226-91589276	Hela-S3	cervix:	n/a
3	chr10:91589226-91589276	NH-A	brain:	n/a
4	chr10:91589226-91589276	Caco-2	colon:	n/a
5	chr10:91589226-91589276	AG09319	gingival:	n/a
6	chr10:91589226-91589276	HEK293	kidney:	embryo
7	chr10:91589226-91589276	BE2_C	brain:	n/a
8	chr10:91589226-91589276	MCF10A-Er-Src	breast:	n/a
9	chr10:91589226-91589276	HUVEC	blood vessel:	n/a
10	chr10:91589226-91589276	K562	blood:	n/a
11	chr10:91589226-91589276	H1-hESC	embryonic stem cell:	embryo
12	chr10:91589226-91589276	BJ	skin:	n/a
13	chr10:91589226-91589276	HPAEpiC	pulmonary alveolar:	n/a
14	chr10:91589226-91589276	GM06990	blood:	n/a
15	chr10:91589226-91589276	HepG2	liver:	n/a
16	chr10:91589226-91589276	MCF-7	breast:	n/a
17	chr10:91589226-91589276	HNPCEpiC	eye:	n/a
18	chr10:91589226-91589276	AG10803	skin:	n/a
19	chr10:91589226-91589276	NB4	blood:	n/a
20	chr10:91589226-91589276	LNCaP	prostate:	n/a
21	chr10:91589226-91589276	HMEC	breast:	n/a
22	chr10:91589226-91589276	HCT-116	colon:	n/a
23	chr10:91589226-91589276	NHDF-neo	bronchial:	n/a
24	chr10:91589226-91589276	GM12891	blood:	n/a
25	chr10:91589226-91589276	HRPEpiC	eye:	n/a
26	chr10:91589226-91589276	HCM	heart:	n/a
27	chr10:91589226-91589276	PFSK-1	brain:	n/a
28	chr10:91589226-91589276	AG04449	skin:	fetal
29	chr10:91589226-91589276	SAEC	small airway:	n/a
30	chr10:91589226-91589276	HCF	heart:	n/a
31	chr10:91589226-91589276	HIPEpiC	eye:	n/a
32	chr10:91589226-91589276	PrEC	prostate:	n/a
33	chr10:91589226-91589276	A549	lung:	n/a
34	chr10:91589226-91589276	U87	brain:	n/a
35	chr10:91589226-91589276	SK-N-SH	brain:	n/a
36	chr10:91589226-91589276	Hepatocyte	liver:	n/a
37	chr10:91589226-91589276	HRCEpiC	kidney:	n/a
38	chr10:91589226-91589276	NHBE	bronchial:	n/a
39	chr10:91589226-91589276	AG09309	skin:	n/a
40	chr10:91589226-91589276	ECC-1	luminal epithelium:	n/a
41	chr10:91589226-91589276	HEEpiC	esophagus:	n/a
42	chr10:91589226-91589276	AoSMC	blood vessel:	n/a
43	chr10:91589226-91589276	HL-60	blood:	n/a
44	chr10:91589226-91589276	RPTEC	kidney:	n/a
45	chr10:91589226-91589276	SK-N-SH_RA	brain:	n/a
46	chr10:91589226-91589276	ovcar-3	ovarian:	n/a
47	chr10:91589226-91589276	HAEpiC	amniotic membrane:	n/a
48	chr10:91589226-91589276	CMK	blood:	n/a
49	chr10:91589226-91589276	HRE	kidney:	n/a
50	chr10:91589226-91589276	T-47D	breast:	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF20B-2	chr10:91586955-91590598	NONHSAT015541
2	lnc-KIF20B-2	chr10:91586955-91590598	NONHSAT015542

No data

Variant related genes	Relation type
LINC00865	TF binding region
LINC00865	CpG island

Extended variants
information (count: 76 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1125326	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12240414	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12244597	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252414	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12263026	0.82[EUR][1000 genomes]
rs12763878	0.95[ASN][1000 genomes]
rs12763984	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12766364	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12770938	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12773439	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12775585	0.98[EUR][1000 genomes]
rs1326198	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1326199	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408582	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17127746	0.85[EUR][1000 genomes]
rs17127968	0.83[EUR][1000 genomes]
rs17128049	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17128178	0.93[ASN][1000 genomes]
rs17385594	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2148276	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2181946	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2182397	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34395627	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34407717	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34498741	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34498979	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34548995	0.88[EUR][1000 genomes]
rs34833458	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35305443	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35494197	0.85[EUR][1000 genomes]
rs35495765	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35557724	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35569149	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35606974	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35762262	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35768372	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36067049	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36075457	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740040	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802651	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55932503	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55977662	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56246606	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56318801	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57160906	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57529292	0.81[EUR][1000 genomes]
rs57585079	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57603165	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58929000	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58933281	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60634654	0.82[EUR][1000 genomes]
rs60925336	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61128077	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61303211	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61646033	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61869791	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61869800	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61869806	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68147789	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7076194	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7098084	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7475158	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7895272	0.85[EUR][1000 genomes]
rs7895851	0.85[EUR][1000 genomes]
rs7895863	0.85[EUR][1000 genomes]
rs7899499	0.85[EUR][1000 genomes]
rs7908739	0.88[EUR][1000 genomes]
rs7908779	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7908953	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7912390	0.82[EUR][1000 genomes];0.93[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	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs58250931	LINC00865	cis	Esophagus Muscularis	GTEx
rs58250931	RP11-248C1.3	cis	Adipose Subcutaneous	GTEx
rs58250931	RP11-248C1.3	cis	lung	GTEx
rs58250931	LINC00865	cis	Nerve Tibial	GTEx
rs58250931	LINC00865	cis	Artery Tibial	GTEx
rs58250931	RP11-248C1.3	cis	Thyroid	GTEx
rs58250931	LINC00865	cis	Thyroid	GTEx
rs58250931	LINC00865	cis	Artery Aorta	GTEx
rs58250931	LINC00865	cis	lung	GTEx
rs58250931	RP11-248C1.3	cis	Artery Tibial	GTEx
rs58250931	LINC00865	cis	Adipose Subcutaneous	GTEx
rs58250931	RP11-248C1.3	cis	Artery Aorta	GTEx
rs58250931	LINC00865	cis	Skin Sun Exposed Lower leg	GTEx
rs58250931	RP11-248C1.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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