Variant report

Variant	rs249449
Chromosome Location	chr5:5033327-5033328
allele	A/C
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:1)
LncRNA
region (count:0)
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	POLR2A	chr5:5033218-5033333	Gliobla	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:5033311-5033361	H1-hESC	embryonic stem cell:	embryo
2	chr5:5033311-5033361	AG09309	skin:	n/a
3	chr5:5033311-5033361	HAEpiC	amniotic membrane:	n/a
4	chr5:5033311-5033361	HepG2	liver:	n/a
5	chr5:5033311-5033361	SKMC	muscle:	n/a
6	chr5:5033311-5033361	AG10803	skin:	n/a
7	chr5:5033311-5033361	RPTEC	kidney:	n/a
8	chr5:5033311-5033361	MCF10A-Er-Src	breast:	n/a
9	chr5:5033311-5033361	Caco-2	colon:	n/a
10	chr5:5033311-5033361	Hela-S3	cervix:	n/a
11	chr5:5033311-5033361	HCT-116	colon:	n/a
12	chr5:5033311-5033361	AoSMC	blood vessel:	n/a
13	chr5:5033311-5033361	U87	brain:	n/a
14	chr5:5033311-5033361	NT2-D1	testis:	n/a
15	chr5:5033311-5033361	HMEC	breast:	n/a
16	chr5:5033311-5033361	GM12878	blood:	n/a
17	chr5:5033311-5033361	SK-N-SH_RA	brain:	n/a
18	chr5:5033311-5033361	HNPCEpiC	eye:	n/a
19	chr5:5033311-5033361	BE2_C	brain:	n/a
20	chr5:5033311-5033361	NHBE	bronchial:	n/a
21	chr5:5033311-5033361	ovcar-3	ovarian:	n/a
22	chr5:5033311-5033361	NH-A	brain:	n/a
23	chr5:5033311-5033361	Jurkat	blood:	n/a
24	chr5:5033311-5033361	SK-N-SH	brain:	n/a
25	chr5:5033311-5033361	HPAEpiC	pulmonary alveolar:	n/a
26	chr5:5033311-5033361	GM12891	blood:	n/a
27	chr5:5033311-5033361	CMK	blood:	n/a
28	chr5:5033311-5033361	PFSK-1	brain:	n/a
29	chr5:5033311-5033361	GM19239	blood:	n/a
30	chr5:5033311-5033361	NB4	blood:	n/a
31	chr5:5033311-5033361	HEK293	kidney:	embryo
32	chr5:5033311-5033361	BJ	skin:	n/a
33	chr5:5033311-5033361	AG09319	gingival:	n/a
34	chr5:5033311-5033361	GM06990	blood:	n/a
35	chr5:5033311-5033361	ProgFib	skin:	n/a
36	chr5:5033311-5033361	LNCaP	prostate:	n/a
37	chr5:5033311-5033361	A549	lung:	n/a
38	chr5:5033311-5033361	PrEC	prostate:	n/a
39	chr5:5033311-5033361	SAEC	small airway:	n/a
40	chr5:5033311-5033361	IMR90	lung:	fetal
41	chr5:5033311-5033361	HCM	heart:	n/a
42	chr5:5033311-5033361	ECC-1	luminal epithelium:	n/a
43	chr5:5033311-5033361	T-47D	breast:	n/a
44	chr5:5033311-5033361	HRE	kidney:	n/a
45	chr5:5033311-5033361	MCF-7	breast:	n/a
46	chr5:5033311-5033361	NHDF-neo	bronchial:	n/a
47	chr5:5033311-5033361	AG04450	lung:	fetal
48	chr5:5033311-5033361	HUVEC	blood vessel:	n/a
49	chr5:5033311-5033361	AG04449	skin:	fetal
50	chr5:5033311-5033361	K562	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:5021569..5024371-chr5:5031180..5034159,2	K562	blood:

No data

Variant related genes	Relation type
LINC01020	TF binding region
LINC01020	CpG island

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10056566	1.00[CEU][hapmap]
rs10067991	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512763	1.00[CEU][hapmap]
rs11951905	1.00[CEU][hapmap]
rs16874638	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs16874650	1.00[CEU][hapmap]
rs171607	1.00[CEU][hapmap]
rs173625	0.96[EUR][1000 genomes]
rs249451	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249454	1.00[CEU][hapmap]
rs249456	1.00[CEU][hapmap]
rs249463	0.96[EUR][1000 genomes]
rs249464	0.96[EUR][1000 genomes]
rs249465	0.96[EUR][1000 genomes]
rs249468	0.96[EUR][1000 genomes]
rs249469	0.96[EUR][1000 genomes]
rs249474	0.92[EUR][1000 genomes]
rs30484	0.96[EUR][1000 genomes]
rs419611	0.96[EUR][1000 genomes]
rs457382	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464252	0.96[EUR][1000 genomes]
rs465434	0.96[EUR][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	nsv1021653	chr5:4932992-5201887	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2757980	chr5:4980876-5184615	Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2759318	chr5:4980876-5184615	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv880436	chr5:4982643-5038540	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv830194	chr5:5002459-5187667	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5033200-5033800	Enhancers	Adipose Nuclei	Adipose
2	chr5:5033200-5034000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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