Variant report

Variant	rs6673420
Chromosome Location	chr1:152814859-152814860
allele	C/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	chr1:152814831-152814881	CMK	blood:	n/a
2	chr1:152814831-152814881	Jurkat	blood:	n/a
3	chr1:152814831-152814881	Hepatocyte	liver:	n/a
4	chr1:152814831-152814881	AG04450	lung:	fetal
5	chr1:152814831-152814881	HRCEpiC	kidney:	n/a
6	chr1:152814831-152814881	PANC-1	pancreas:	n/a
7	chr1:152814831-152814881	HCF	heart:	n/a
8	chr1:152814831-152814881	SK-N-MC	brain:	n/a
9	chr1:152814831-152814881	SAEC	small airway:	n/a
10	chr1:152814831-152814881	PrEC	prostate:	n/a
11	chr1:152814831-152814881	AG09319	gingival:	n/a
12	chr1:152814831-152814881	ovcar-3	ovarian:	n/a
13	chr1:152814831-152814881	HCT-116	colon:	n/a
14	chr1:152814831-152814881	U87	brain:	n/a
15	chr1:152814831-152814881	HNPCEpiC	eye:	n/a
16	chr1:152814831-152814881	IMR90	lung:	fetal
17	chr1:152814831-152814881	NT2-D1	testis:	n/a
18	chr1:152814831-152814881	GM06990	blood:	n/a
19	chr1:152814831-152814881	AG10803	skin:	n/a
20	chr1:152814831-152814881	RPTEC	kidney:	n/a
21	chr1:152814831-152814881	NH-A	brain:	n/a
22	chr1:152814831-152814881	HIPEpiC	eye:	n/a
23	chr1:152814831-152814881	K562	blood:	n/a
24	chr1:152814831-152814881	HRE	kidney:	n/a
25	chr1:152814831-152814881	ECC-1	luminal epithelium:	n/a
26	chr1:152814831-152814881	HAEpiC	amniotic membrane:	n/a
27	chr1:152814831-152814881	SK-N-SH_RA	brain:	n/a
28	chr1:152814831-152814881	MCF-7	breast:	n/a
29	chr1:152814831-152814881	Caco-2	colon:	n/a
30	chr1:152814831-152814881	SKMC	muscle:	n/a
31	chr1:152814831-152814881	BE2_C	brain:	n/a
32	chr1:152814831-152814881	BJ	skin:	n/a
33	chr1:152814831-152814881	HUVEC	blood vessel:	n/a
34	chr1:152814831-152814881	HRPEpiC	eye:	n/a
35	chr1:152814831-152814881	GM12891	blood:	n/a
36	chr1:152814831-152814881	HEK293	kidney:	embryo
37	chr1:152814831-152814881	HCM	heart:	n/a
38	chr1:152814831-152814881	A549	lung:	n/a
39	chr1:152814831-152814881	T-47D	breast:	n/a
40	chr1:152814831-152814881	AG09309	skin:	n/a
41	chr1:152814831-152814881	HL-60	blood:	n/a
42	chr1:152814831-152814881	GM12878	blood:	n/a
43	chr1:152814831-152814881	GM12892	blood:	n/a
44	chr1:152814831-152814881	HMEC	breast:	n/a
45	chr1:152814831-152814881	NHDF-neo	bronchial:	n/a
46	chr1:152814831-152814881	HPAEpiC	pulmonary alveolar:	n/a
47	chr1:152814831-152814881	H1-hESC	embryonic stem cell:	embryo
48	chr1:152814831-152814881	HCPEpiC	choroid plexus:	n/a
49	chr1:152814831-152814881	AG04449	skin:	fetal
50	chr1:152814831-152814881	AoSMC	blood vessel:	n/a

No data

Variant related genes	Relation type
LCE6A	CpG island

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11205115	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11800110	1.00[CEU][hapmap]
rs11804354	1.00[CEU][hapmap]
rs11804404	1.00[CEU][hapmap]
rs11804419	1.00[CEU][hapmap]
rs11805896	1.00[CEU][hapmap]
rs11809092	1.00[CEU][hapmap]
rs11810194	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12073467	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs16834574	1.00[CEU][hapmap]
rs16834582	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs16834595	1.00[CEU][hapmap]
rs16834596	1.00[CEU][hapmap]
rs16834611	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs16834719	1.00[CEU][hapmap]
rs16834732	1.00[CEU][hapmap]
rs2339389	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339390	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2339393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3906158	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378153	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6674372	1.00[CEU][hapmap]
rs6684782	1.00[CEU][hapmap]
rs6699386	1.00[CEU][hapmap]
rs6703505	1.00[CEU][hapmap]
rs73019084	1.00[EUR][1000 genomes]
rs73021109	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73021166	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73021168	1.00[EUR][1000 genomes]
rs73021171	1.00[EUR][1000 genomes]
rs7519200	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7531043	1.00[EUR][1000 genomes]
rs7538584	1.00[EUR][1000 genomes]
rs7540269	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7541578	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7550874	0.90[AFR][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

Quick Search:

Input of quick search could be:

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links