Variant report

Variant	rs6049286
Chromosome Location	chr20:23972452-23972453
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	chr20:23972451-23972501	BE2_C	brain:	n/a
2	chr20:23972451-23972501	AoSMC	blood vessel:	n/a
3	chr20:23972451-23972501	HUVEC	blood vessel:	n/a
4	chr20:23972451-23972501	K562	blood:	n/a
5	chr20:23972451-23972501	HRCEpiC	kidney:	n/a
6	chr20:23972451-23972501	HCPEpiC	choroid plexus:	n/a
7	chr20:23972451-23972501	GM12878	blood:	n/a
8	chr20:23972451-23972501	GM12891	blood:	n/a
9	chr20:23972451-23972501	HPAEpiC	pulmonary alveolar:	n/a
10	chr20:23972451-23972501	AG04450	lung:	fetal
11	chr20:23972451-23972501	IMR90	lung:	fetal
12	chr20:23972451-23972501	BJ	skin:	n/a
13	chr20:23972451-23972501	U87	brain:	n/a
14	chr20:23972451-23972501	AG10803	skin:	n/a
15	chr20:23972451-23972501	HCF	heart:	n/a
16	chr20:23972451-23972501	PrEC	prostate:	n/a
17	chr20:23972451-23972501	Caco-2	colon:	n/a
18	chr20:23972451-23972501	HL-60	blood:	n/a
19	chr20:23972451-23972501	SK-N-SH	brain:	n/a
20	chr20:23972451-23972501	Hela-S3	cervix:	n/a
21	chr20:23972451-23972501	SAEC	small airway:	n/a
22	chr20:23972451-23972501	HMEC	breast:	n/a
23	chr20:23972451-23972501	NHDF-neo	bronchial:	n/a
24	chr20:23972451-23972501	H1-hESC	embryonic stem cell:	embryo
25	chr20:23972451-23972501	ProgFib	skin:	n/a
26	chr20:23972451-23972501	HRE	kidney:	n/a
27	chr20:23972451-23972501	ovcar-3	ovarian:	n/a
28	chr20:23972451-23972501	ECC-1	luminal epithelium:	n/a
29	chr20:23972451-23972501	NB4	blood:	n/a
30	chr20:23972451-23972501	GM06990	blood:	n/a
31	chr20:23972451-23972501	GM12892	blood:	n/a
32	chr20:23972451-23972501	NH-A	brain:	n/a
33	chr20:23972451-23972501	HIPEpiC	eye:	n/a
34	chr20:23972451-23972501	T-47D	breast:	n/a
35	chr20:23972451-23972501	SKMC	muscle:	n/a
36	chr20:23972451-23972501	HNPCEpiC	eye:	n/a
37	chr20:23972451-23972501	HEEpiC	esophagus:	n/a
38	chr20:23972451-23972501	NHBE	bronchial:	n/a
39	chr20:23972451-23972501	NT2-D1	testis:	n/a
40	chr20:23972451-23972501	Hepatocyte	liver:	n/a
41	chr20:23972451-23972501	HCM	heart:	n/a
42	chr20:23972451-23972501	SK-N-SH_RA	brain:	n/a
43	chr20:23972451-23972501	GM19239	blood:	n/a
44	chr20:23972451-23972501	MCF-7	breast:	n/a
45	chr20:23972451-23972501	HAEpiC	amniotic membrane:	n/a
46	chr20:23972451-23972501	CMK	blood:	n/a
47	chr20:23972451-23972501	AG09319	gingival:	n/a
48	chr20:23972451-23972501	Jurkat	blood:	n/a
49	chr20:23972451-23972501	SK-N-MC	brain:	n/a
50	chr20:23972451-23972501	A549	lung:	n/a

No data

Variant related genes	Relation type
GGTLC1	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs6036598	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049287	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73328709	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833944	chr20:23806288-24021865	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1063474	chr20:23918394-24048069	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1056491	chr20:23955040-24105080	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv15775	chr20:23955662-23977093	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv820636	chr20:23956042-23976910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv18738	chr20:23956042-23994680	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv1806279	chr20:23956609-23980100	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv962565	chr20:23956974-23976574	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv962598	chr20:23971365-23976074	Inactive region	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
12	esv16644	chr20:23971832-23976616	Inactive region	TF binding region CpG island Chromatin interactive region	1 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