Variant report

Variant	rs420010
Chromosome Location	chr11:5508810-5508811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr11:5508702-5508901	K562	blood:	n/a	n/a
2	POLR2A	chr11:5508617-5509537	K562	blood:	n/a	n/a
3	POLR2A	chr11:5504855-5512186	K562	blood:	n/a	n/a
4	POLR2A	chr11:5507590-5509519	K562	blood:	n/a	n/a
5	POLR2A	chr11:5508571-5509183	K562	blood:	n/a	n/a
6	POLR2A	chr11:5508551-5511479	K562	blood:	n/a	n/a
7	E2F4	chr11:5508771-5508940	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr11:5506384-5509626	K562	blood:	n/a	n/a
9	POLR2A	chr11:5508644-5511487	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:5508789-5508839	SK-N-SH	brain:	n/a
2	chr11:5508789-5508839	HMEC	breast:	n/a
3	chr11:5508789-5508839	HCT-116	colon:	n/a
4	chr11:5508789-5508839	GM12878	blood:	n/a
5	chr11:5508789-5508839	CMK	blood:	n/a
6	chr11:5508789-5508839	SKMC	muscle:	n/a
7	chr11:5508789-5508839	RPTEC	kidney:	n/a
8	chr11:5508789-5508839	PrEC	prostate:	n/a
9	chr11:5508789-5508839	HEK293	kidney:	embryo
10	chr11:5508789-5508839	AG04449	skin:	fetal
11	chr11:5508789-5508839	AG09319	gingival:	n/a
12	chr11:5508789-5508839	HNPCEpiC	eye:	n/a
13	chr11:5508789-5508839	BJ	skin:	n/a
14	chr11:5508789-5508839	BE2_C	brain:	n/a
15	chr11:5508789-5508839	K562	blood:	n/a
16	chr11:5508789-5508839	HCF	heart:	n/a
17	chr11:5508789-5508839	ovcar-3	ovarian:	n/a
18	chr11:5508789-5508839	PFSK-1	brain:	n/a
19	chr11:5508789-5508839	Hepatocyte	liver:	n/a
20	chr11:5508789-5508839	HIPEpiC	eye:	n/a
21	chr11:5508789-5508839	HRE	kidney:	n/a
22	chr11:5508789-5508839	AG10803	skin:	n/a
23	chr11:5508789-5508839	GM06990	blood:	n/a
24	chr11:5508789-5508839	HepG2	liver:	n/a
25	chr11:5508789-5508839	GM12891	blood:	n/a
26	chr11:5508789-5508839	HRCEpiC	kidney:	n/a
27	chr11:5508789-5508839	NH-A	brain:	n/a
28	chr11:5508789-5508839	HRPEpiC	eye:	n/a
29	chr11:5508789-5508839	IMR90	lung:	fetal
30	chr11:5508789-5508839	MCF10A-Er-Src	breast:	n/a
31	chr11:5508789-5508839	U87	brain:	n/a
32	chr11:5508789-5508839	ProgFib	skin:	n/a
33	chr11:5508789-5508839	ECC-1	luminal epithelium:	n/a
34	chr11:5508789-5508839	NB4	blood:	n/a
35	chr11:5508789-5508839	SAEC	small airway:	n/a
36	chr11:5508789-5508839	GM12892	blood:	n/a
37	chr11:5508789-5508839	Hela-S3	cervix:	n/a
38	chr11:5508789-5508839	HCM	heart:	n/a
39	chr11:5508789-5508839	T-47D	breast:	n/a
40	chr11:5508789-5508839	HEEpiC	esophagus:	n/a
41	chr11:5508789-5508839	SK-N-SH_RA	brain:	n/a
42	chr11:5508789-5508839	HPAEpiC	pulmonary alveolar:	n/a
43	chr11:5508789-5508839	LNCaP	prostate:	n/a
44	chr11:5508789-5508839	H1-hESC	embryonic stem cell:	embryo
45	chr11:5508789-5508839	SK-N-MC	brain:	n/a
46	chr11:5508789-5508839	HCPEpiC	choroid plexus:	n/a
47	chr11:5508789-5508839	HAEpiC	amniotic membrane:	n/a
48	chr11:5508789-5508839	PANC-1	pancreas:	n/a
49	chr11:5508789-5508839	Jurkat	blood:	n/a
50	chr11:5508789-5508839	HL-60	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:4988858-5002113..11:5505728-5514500	Hela-S3	cervix:

No data

Variant related genes	Relation type
OR52D1	TF binding region
OR52D1	CpG island
ENSG00000225003	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1694677	0.87[YRI][hapmap]
rs2467219	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs317785	0.80[YRI][hapmap]
rs368246	0.83[YRI][hapmap]
rs368661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs369016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs371288	0.86[YRI][hapmap]
rs372091	0.86[YRI][hapmap]
rs372500	0.87[YRI][hapmap]
rs377304	0.86[YRI][hapmap]
rs379616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383387	0.80[YRI][hapmap]
rs392296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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]
rs392736	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394620	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs394893	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs402182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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]
rs409915	0.87[YRI][hapmap]
rs414154	0.86[YRI][hapmap]
rs415009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs417382	0.86[YRI][hapmap]
rs417425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418003	1.00[CHB][hapmap];1.00[JPT][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]
rs418756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs420405	0.80[YRI][hapmap]
rs421126	0.86[YRI][hapmap]
rs422171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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]
rs427381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs428196	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428345	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433202	0.86[YRI][hapmap]
rs444819	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs444878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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]
rs445316	0.87[YRI][hapmap]
rs447358	0.86[YRI][hapmap]
rs447575	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs447591	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs449408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451326	0.86[YRI][hapmap]
rs452713	0.86[YRI][hapmap]
rs453163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][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]
rs454727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910804	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
2	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
4	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1039285	chr11:5504861-5519672	Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1042308	chr11:5504861-5520062	Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv467670	chr11:5506034-5550630	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv553240	chr11:5506034-5550630	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5506600-5510800	Genic enhancers	K562	blood

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