Variant report

Variant	rs17109402
Chromosome Location	chr10:90346479-90346480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:90346479-90346529	AG09319	gingival:	n/a
2	chr10:90346479-90346529	LNCaP	prostate:	n/a
3	chr10:90346479-90346529	HCT-116	colon:	n/a
4	chr10:90346479-90346529	CMK	blood:	n/a
5	chr10:90346479-90346529	GM12878	blood:	n/a
6	chr10:90346479-90346529	ECC-1	luminal epithelium:	n/a
7	chr10:90346479-90346529	HCM	heart:	n/a
8	chr10:90346479-90346529	HRPEpiC	eye:	n/a
9	chr10:90346479-90346529	SKMC	muscle:	n/a
10	chr10:90346479-90346529	HRE	kidney:	n/a
11	chr10:90346479-90346529	MCF-7	breast:	n/a
12	chr10:90346479-90346529	HL-60	blood:	n/a
13	chr10:90346479-90346529	HIPEpiC	eye:	n/a
14	chr10:90346479-90346529	GM12892	blood:	n/a
15	chr10:90346479-90346529	BJ	skin:	n/a
16	chr10:90346479-90346529	AG09309	skin:	n/a
17	chr10:90346479-90346529	HAEpiC	amniotic membrane:	n/a
18	chr10:90346479-90346529	T-47D	breast:	n/a
19	chr10:90346479-90346529	HCPEpiC	choroid plexus:	n/a
20	chr10:90346479-90346529	A549	lung:	n/a
21	chr10:90346479-90346529	HUVEC	blood vessel:	n/a
22	chr10:90346479-90346529	HNPCEpiC	eye:	n/a
23	chr10:90346479-90346529	HMEC	breast:	n/a
24	chr10:90346479-90346529	HEEpiC	esophagus:	n/a
25	chr10:90346479-90346529	NH-A	brain:	n/a
26	chr10:90346479-90346529	MCF10A-Er-Src	breast:	n/a
27	chr10:90346479-90346529	HepG2	liver:	n/a
28	chr10:90346479-90346529	AoSMC	blood vessel:	n/a
29	chr10:90346479-90346529	U87	brain:	n/a
30	chr10:90346479-90346529	SAEC	small airway:	n/a
31	chr10:90346479-90346529	NHBE	bronchial:	n/a
32	chr10:90346479-90346529	HEK293	kidney:	embryo
33	chr10:90346479-90346529	SK-N-MC	brain:	n/a
34	chr10:90346479-90346529	GM19239	blood:	n/a
35	chr10:90346479-90346529	Jurkat	blood:	n/a
36	chr10:90346479-90346529	K562	blood:	n/a
37	chr10:90346479-90346529	PFSK-1	brain:	n/a
38	chr10:90346479-90346529	Caco-2	colon:	n/a
39	chr10:90346479-90346529	HPAEpiC	pulmonary alveolar:	n/a
40	chr10:90346479-90346529	RPTEC	kidney:	n/a
41	chr10:90346479-90346529	ProgFib	skin:	n/a
42	chr10:90346479-90346529	SK-N-SH_RA	brain:	n/a
43	chr10:90346479-90346529	IMR90	lung:	fetal
44	chr10:90346479-90346529	NT2-D1	testis:	n/a
45	chr10:90346479-90346529	HRCEpiC	kidney:	n/a
46	chr10:90346479-90346529	GM06990	blood:	n/a
47	chr10:90346479-90346529	Hela-S3	cervix:	n/a
48	chr10:90346479-90346529	AG10803	skin:	n/a
49	chr10:90346479-90346529	NHDF-neo	bronchial:	n/a
50	chr10:90346479-90346529	Hepatocyte	liver:	n/a

No data

Variant related genes	Relation type
RNLS	CpG island
LIPJ	CpG island
ENSG00000201548	CpG island

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10694823	1.00[ASN][1000 genomes]
rs1325899	1.00[CHB][hapmap]
rs17109303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs17109478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs17109533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17109578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110995	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17111000	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17111050	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17113316	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2861367	1.00[CHB][hapmap]
rs41298235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41299155	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41306844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57841856	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59420228	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1044680	chr10:90316066-90466092	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv540740	chr10:90316066-90466092	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1037657	chr10:90329910-90367890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv551839	chr10:90334835-90422136	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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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