Variant report

Variant	rs16834602
Chromosome Location	chr1:152814309-152814310
allele	A/G
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	chr1:152814273-152814323	GM06990	blood:	n/a
2	chr1:152814273-152814323	HIPEpiC	eye:	n/a
3	chr1:152814273-152814323	BJ	skin:	n/a
4	chr1:152814273-152814323	LNCaP	prostate:	n/a
5	chr1:152814273-152814323	AG09319	gingival:	n/a
6	chr1:152814273-152814323	A549	lung:	n/a
7	chr1:152814273-152814323	RPTEC	kidney:	n/a
8	chr1:152814273-152814323	MCF-7	breast:	n/a
9	chr1:152814273-152814323	HCF	heart:	n/a
10	chr1:152814273-152814323	NT2-D1	testis:	n/a
11	chr1:152814273-152814323	Caco-2	colon:	n/a
12	chr1:152814273-152814323	BE2_C	brain:	n/a
13	chr1:152814273-152814323	PFSK-1	brain:	n/a
14	chr1:152814273-152814323	SAEC	small airway:	n/a
15	chr1:152814273-152814323	Jurkat	blood:	n/a
16	chr1:152814273-152814323	AG04450	lung:	fetal
17	chr1:152814273-152814323	NB4	blood:	n/a
18	chr1:152814273-152814323	HEK293	kidney:	embryo
19	chr1:152814273-152814323	HL-60	blood:	n/a
20	chr1:152814273-152814323	NHDF-neo	bronchial:	n/a
21	chr1:152814273-152814323	U87	brain:	n/a
22	chr1:152814273-152814323	T-47D	breast:	n/a
23	chr1:152814273-152814323	GM12878	blood:	n/a
24	chr1:152814273-152814323	HRCEpiC	kidney:	n/a
25	chr1:152814273-152814323	HEEpiC	esophagus:	n/a
26	chr1:152814273-152814323	Hepatocyte	liver:	n/a
27	chr1:152814273-152814323	MCF10A-Er-Src	breast:	n/a
28	chr1:152814273-152814323	HRE	kidney:	n/a
29	chr1:152814273-152814323	AG04449	skin:	fetal
30	chr1:152814273-152814323	AoSMC	blood vessel:	n/a
31	chr1:152814273-152814323	GM12891	blood:	n/a
32	chr1:152814273-152814323	SKMC	muscle:	n/a
33	chr1:152814273-152814323	GM12892	blood:	n/a
34	chr1:152814273-152814323	NHBE	bronchial:	n/a
35	chr1:152814273-152814323	GM19239	blood:	n/a
36	chr1:152814273-152814323	HCT-116	colon:	n/a
37	chr1:152814273-152814323	SK-N-MC	brain:	n/a
38	chr1:152814273-152814323	AG09309	skin:	n/a
39	chr1:152814273-152814323	SK-N-SH_RA	brain:	n/a
40	chr1:152814273-152814323	HMEC	breast:	n/a
41	chr1:152814273-152814323	Hela-S3	cervix:	n/a
42	chr1:152814273-152814323	PANC-1	pancreas:	n/a
43	chr1:152814273-152814323	HCM	heart:	n/a
44	chr1:152814273-152814323	AG10803	skin:	n/a
45	chr1:152814273-152814323	HPAEpiC	pulmonary alveolar:	n/a
46	chr1:152814273-152814323	HRPEpiC	eye:	n/a
47	chr1:152814273-152814323	NH-A	brain:	n/a
48	chr1:152814273-152814323	HAEpiC	amniotic membrane:	n/a
49	chr1:152814273-152814323	K562	blood:	n/a
50	chr1:152814273-152814323	CMK	blood:	n/a

No data

Variant related genes	Relation type
LCE6A	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10494279	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1411618	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16834568	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs16834601	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16834669	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16834672	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16834674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16834681	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16834684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1819431	0.86[AFR][1000 genomes]
rs1819432	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339391	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339392	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6696383	1.00[YRI][hapmap]
rs6696504	1.00[YRI][hapmap]
rs73008517	1.00[EUR][1000 genomes]
rs73019083	1.00[EUR][1000 genomes]
rs73019089	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73019090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73021107	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73021172	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73021184	1.00[EUR][1000 genomes]
rs73023043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023054	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023059	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023065	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7542269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7553765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
9	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1009885	chr1:152762750-152851273	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1010576	chr1:152791716-152827652	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1000159	chr1:152809514-152853766	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1008447	chr1:152811171-152853748	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	esv2761937	chr1:152811183-152853760	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 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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