Variant report

Variant	rs4492907
Chromosome Location	chr12:117630765-117630766
allele	C/T
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	chr12:117630719-117630769	HRCEpiC	kidney:	n/a
2	chr12:117630719-117630769	HCT-116	colon:	n/a
3	chr12:117630719-117630769	A549	lung:	n/a
4	chr12:117630719-117630769	CMK	blood:	n/a
5	chr12:117630719-117630769	AG09319	gingival:	n/a
6	chr12:117630719-117630769	HUVEC	blood vessel:	n/a
7	chr12:117630719-117630769	RPTEC	kidney:	n/a
8	chr12:117630719-117630769	GM12891	blood:	n/a
9	chr12:117630719-117630769	PrEC	prostate:	n/a
10	chr12:117630719-117630769	SK-N-SH	brain:	n/a
11	chr12:117630719-117630769	GM12878	blood:	n/a
12	chr12:117630719-117630769	NH-A	brain:	n/a
13	chr12:117630719-117630769	ProgFib	skin:	n/a
14	chr12:117630719-117630769	AG10803	skin:	n/a
15	chr12:117630719-117630769	Hela-S3	cervix:	n/a
16	chr12:117630719-117630769	IMR90	lung:	fetal
17	chr12:117630719-117630769	HEEpiC	esophagus:	n/a
18	chr12:117630719-117630769	HepG2	liver:	n/a
19	chr12:117630719-117630769	HEK293	kidney:	embryo
20	chr12:117630719-117630769	AG04450	lung:	fetal
21	chr12:117630719-117630769	HCM	heart:	n/a
22	chr12:117630719-117630769	HL-60	blood:	n/a
23	chr12:117630719-117630769	HAEpiC	amniotic membrane:	n/a
24	chr12:117630719-117630769	AG04449	skin:	fetal
25	chr12:117630719-117630769	SKMC	muscle:	n/a
26	chr12:117630719-117630769	HCPEpiC	choroid plexus:	n/a
27	chr12:117630719-117630769	GM19239	blood:	n/a
28	chr12:117630719-117630769	SK-N-SH_RA	brain:	n/a
29	chr12:117630719-117630769	GM12892	blood:	n/a
30	chr12:117630719-117630769	Jurkat	blood:	n/a
31	chr12:117630719-117630769	HNPCEpiC	eye:	n/a
32	chr12:117630719-117630769	HRE	kidney:	n/a
33	chr12:117630719-117630769	ECC-1	luminal epithelium:	n/a
34	chr12:117630719-117630769	NT2-D1	testis:	n/a
35	chr12:117630719-117630769	ovcar-3	ovarian:	n/a
36	chr12:117630719-117630769	U87	brain:	n/a
37	chr12:117630719-117630769	SK-N-MC	brain:	n/a
38	chr12:117630719-117630769	AG09309	skin:	n/a
39	chr12:117630719-117630769	MCF-7	breast:	n/a
40	chr12:117630719-117630769	SAEC	small airway:	n/a
41	chr12:117630719-117630769	PFSK-1	brain:	n/a
42	chr12:117630719-117630769	HMEC	breast:	n/a
43	chr12:117630719-117630769	BE2_C	brain:	n/a
44	chr12:117630719-117630769	LNCaP	prostate:	n/a
45	chr12:117630719-117630769	K562	blood:	n/a
46	chr12:117630719-117630769	AoSMC	blood vessel:	n/a
47	chr12:117630719-117630769	NB4	blood:	n/a
48	chr12:117630719-117630769	Caco-2	colon:	n/a
49	chr12:117630719-117630769	HRPEpiC	eye:	n/a
50	chr12:117630719-117630769	PANC-1	pancreas:	n/a

No data

Variant related genes	Relation type
FBXO21	CpG island

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10774905	0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs10850774	0.86[ASN][1000 genomes]
rs10850777	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs10850782	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs10850786	0.82[EUR][1000 genomes]
rs10850790	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10850799	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11068369	0.80[EUR][1000 genomes]
rs11068370	0.80[EUR][1000 genomes]
rs11068371	0.80[EUR][1000 genomes]
rs12304875	0.82[EUR][1000 genomes]
rs12310778	0.81[EUR][1000 genomes]
rs12322298	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs12422378	0.81[EUR][1000 genomes]
rs1472522	0.89[CEU][hapmap]
rs2036311	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2036312	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2062518	0.82[EUR][1000 genomes]
rs2062530	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2088699	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2840100	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3741472	0.80[EUR][1000 genomes]
rs4238053	0.82[EUR][1000 genomes]
rs4766831	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4766834	0.84[EUR][1000 genomes]
rs4767502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767503	0.81[EUR][1000 genomes]
rs4767504	0.81[EUR][1000 genomes]
rs4767505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4767506	0.81[EUR][1000 genomes]
rs4767507	0.81[EUR][1000 genomes]
rs4767511	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs4767512	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767514	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4767515	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4767518	0.91[EUR][1000 genomes]
rs4767519	0.86[EUR][1000 genomes]
rs6490117	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67383912	0.89[EUR][1000 genomes]
rs7297713	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307866	0.84[ASN][1000 genomes]
rs7313745	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953808	0.88[ASN][1000 genomes]
rs7957758	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884282	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3409292	chr12:117613281-117638743	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
3	nsv510592	chr12:117618872-117684713	Bivalent/Poised TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv560346	chr12:117623651-117642113	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	nsv560347	chr12:117623651-117643067	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	esv1844687	chr12:117630765-117643067	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	esv1844732	chr12:117630765-117643067	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv560348	chr12:117630765-117643067	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4492907	FBXO21	Cis_1M	lymphoblastoid	RTeQTL
rs4492907	C12orf51	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117628400-117635200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:117628800-117633200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:117629000-117641000	Weak transcription	Spleen	Spleen
4	chr12:117630400-117633200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:117630600-117633000	Weak transcription	Hela-S3	cervix

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