Variant report

Variant	rs2814086
Chromosome Location	chr1:227669393-227669394
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:233)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:233 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:227669300-227669450	NHLF	lung:	n/a	n/a
2	CTCF	chr1:227669250-227669559	K562	blood:	n/a	n/a
3	CTCF	chr1:227669260-227669410	HFF-Myc	foreskin:	n/a	n/a
4	CTCF	chr1:227669340-227669490	GM12878	blood:	n/a	n/a
5	ZNF143	chr1:227669238-227669635	GM12878	blood:	n/a	n/a
6	CTCF	chr1:227669340-227669490	HPF	lung:	n/a	n/a
7	CTCF	chr1:227669300-227669450	GM12866	blood:	n/a	n/a
8	CTCF	chr1:227669294-227669528	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:227669340-227669490	Caco-2	colon:	n/a	n/a
10	CTCF	chr1:227669336-227669534	A549	lung:	n/a	n/a
11	CTCF	chr1:227669298-227669502	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr1:227669340-227669490	HEEpiC	esophagus:	n/a	n/a
13	POLR2A	chr1:227669275-227669583	IMR90	lung:	n/a	n/a
14	MYC	chr1:227669298-227669620	K562	blood:	n/a	n/a
15	CTCF	chr1:227669284-227669539	GM10248	blood:	n/a	n/a
16	CTCF	chr1:227669273-227669549	GM13977	blood:	n/a	n/a
17	CTCF	chr1:227669360-227669510	AG04449	skin:	n/a	n/a
18	CTCF	chr1:227669340-227669490	GM12864	blood:	n/a	n/a
19	MYC	chr1:227669268-227669581	MCF10A-Er-Src	breast:	n/a	n/a
20	RAD21	chr1:227669043-227669943	SK-N-SH	brain:	n/a	chr1:227669762-227669774
21	CTCF	chr1:227669380-227669530	MCF-7	breast:	n/a	n/a
22	CTCF	chr1:227669380-227669530	HMEC	breast:	n/a	n/a
23	RAD21	chr1:227669215-227669694	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr1:227669380-227669530	AG04450	lung:	n/a	n/a
25	RAD21	chr1:227669250-227669758	MCF-7	breast:	n/a	n/a
26	CTCF	chr1:227669270-227669572	K562	blood:	n/a	n/a
27	ZNF143	chr1:227669250-227669592	K562	blood:	n/a	n/a
28	CTCF	chr1:227669360-227669510	A549	lung:	n/a	n/a
29	CTCF	chr1:227669320-227669470	HepG2	liver:	n/a	n/a
30	CTCF	chr1:227669051-227669769	A549	lung:	n/a	n/a
31	CTCF	chr1:227669306-227669535	GM20000	blood:	n/a	n/a
32	CTCF	chr1:227669293-227669538	GM19239	blood:	n/a	n/a
33	CTCF	chr1:227669360-227669510	HEEpiC	esophagus:	n/a	n/a
34	CTCF	chr1:227669360-227669510	HVMF	connective:	n/a	n/a
35	RAD21	chr1:227669194-227669848	HCT-116	colon:	n/a	chr1:227669762-227669774
36	CTCF	chr1:227669300-227669450	HRPEpiC	eye:	n/a	n/a
37	GATA3	chr1:227669240-227669604	T-47D	breast:	n/a	n/a
38	SMC3	chr1:227669145-227669843	SK-N-SH	brain:	n/a	n/a
39	STAT3	chr1:227669372-227669503	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr1:227669300-227669450	GM12872	blood:	n/a	n/a
41	CTCF	chr1:227669195-227669674	MCF-7	breast:	n/a	n/a
42	CTCF	chr1:227669360-227669510	BJ	skin:	n/a	n/a
43	CTCF	chr1:227669340-227669490	GM12801	blood:	n/a	n/a
44	CTCF	chr1:227669340-227669490	HAc	cerebellar:	n/a	n/a
45	RAD21	chr1:227669133-227669777	H1-hESC	embryonic stem cell:	n/a	chr1:227669762-227669774
46	CTCF	chr1:227669340-227669490	BJ	skin:	n/a	n/a
47	CTCF	chr1:227669340-227669490	HBMEC	blood vessel:	n/a	n/a
48	CTCF	chr1:227669340-227669490	HCM	heart:	n/a	n/a
49	CTCF	chr1:227669320-227669470	NHDF-neo	bronchial:	n/a	n/a
50	RAD21	chr1:227669260-227669603	A549	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227669292..227669934-chr1:228141333..228142021,4	K562	blood:
2	chr1:227669108..227669644-chr1:228318559..228319309,2	K562	blood:
3	chr1:227667899..227669532-chr1:227915854..227918732,2	MCF-7	breast:
4	chr1:227669242..227673785-chr1:227914780..227918377,5	MCF-7	breast:
5	chr1:227669109..227669887-chr1:228134058..228134849,3	K562	blood:
6	chr1:227668674..227670909-chr1:228132996..228135625,2	K562	blood:
7	chr1:227668984..227669861-chr1:228133992..228134634,2	MCF-7	breast:
8	chr1:227668951..227669884-chr1:227949577..227950975,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237193	TF binding region
ENSG00000143740	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10799420	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10799421	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10916148	0.81[AMR][1000 genomes]
rs10916150	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12128670	0.81[AMR][1000 genomes]
rs1390403	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495850	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2819522	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819524	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61833893	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61833894	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7549565	0.90[EUR][1000 genomes]
rs9628651	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2814086	ZNF678	cis	cerebellum	SCAN
rs2814086	OBSCN	cis	cerebellum	SCAN
rs2814086	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs2814086	CDC42BPA	cis	cerebellum	SCAN

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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