Variant report

Variant	rs7314888
Chromosome Location	chr12:10456924-10456925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:10456755-10457020	Hela-S3	cervix:	n/a	n/a
2	BCL3	chr12:10456668-10457144	GM12878	blood:	n/a	n/a
3	MAFK	chr12:10456687-10457039	IMR90	lung:	n/a	n/a
4	BATF	chr12:10456621-10457029	GM12878	blood:	n/a	n/a
5	NFIC	chr12:10456449-10457118	GM12878	blood:	n/a	n/a
6	STAT3	chr12:10456778-10457088	MCF10A-Er-Src	breast:	n/a	chr12:10456979-10456990
7	STAT5A	chr12:10456625-10457024	GM12878	blood:	n/a	n/a
8	FOS	chr12:10456715-10457065	MCF10A-Er-Src	breast:	n/a	n/a
9	NFIC	chr12:10456654-10457112	GM12878	blood:	n/a	n/a
10	FOS	chr12:10456747-10456966	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr12:10456489-10457014	MCF10A-Er-Src	breast:	n/a	chr12:10456979-10456990
12	NFATC1	chr12:10456638-10457130	GM12878	blood:	n/a	n/a
13	IRF4	chr12:10456654-10457029	GM12878	blood:	n/a	n/a
14	STAT3	chr12:10456721-10457132	MCF10A-Er-Src	breast:	n/a	chr12:10456979-10456990
15	RUNX3	chr12:10456526-10457209	GM12878	blood:	n/a	n/a
16	ATF2	chr12:10456577-10457005	GM12878	blood:	n/a	n/a
17	EP300	chr12:10456745-10457040	Hela-S3	cervix:	n/a	n/a
18	FOXM1	chr12:10456544-10457143	GM12878	blood:	n/a	n/a
19	RUNX3	chr12:10456594-10457141	GM12878	blood:	n/a	n/a
20	MTA3	chr12:10456621-10457078	GM12878	blood:	n/a	n/a
21	STAT3	chr12:10456747-10457052	Hela-S3	cervix:	n/a	chr12:10456979-10456990
22	MYC	chr12:10456747-10456937	MCF10A-Er-Src	breast:	n/a	n/a
23	CEBPB	chr12:10456678-10457101	IMR90	lung:	n/a	n/a
24	FOS	chr12:10456643-10457029	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr12:10456727-10457030	MCF10A-Er-Src	breast:	n/a	n/a
26	RFX5	chr12:10456374-10457127	IMR90	lung:	n/a	n/a
27	STAT3	chr12:10456661-10457132	MCF10A-Er-Src	breast:	n/a	chr12:10456979-10456990
28	CHD1	chr12:10456543-10457321	IMR90	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:10456885-10456935	PANC-1	pancreas:	n/a
2	chr12:10456885-10456935	Jurkat	blood:	n/a
3	chr12:10456885-10456935	IMR90	lung:	fetal
4	chr12:10456885-10456935	MCF10A-Er-Src	breast:	n/a
5	chr12:10456885-10456935	NH-A	brain:	n/a
6	chr12:10456885-10456935	PrEC	prostate:	n/a
7	chr12:10456885-10456935	Hepatocyte	liver:	n/a
8	chr12:10456885-10456935	MCF-7	breast:	n/a
9	chr12:10456885-10456935	HEEpiC	esophagus:	n/a
10	chr12:10456885-10456935	AoSMC	blood vessel:	n/a
11	chr12:10456885-10456935	HAEpiC	amniotic membrane:	n/a
12	chr12:10456885-10456935	SKMC	muscle:	n/a
13	chr12:10456885-10456935	GM12892	blood:	n/a
14	chr12:10456885-10456935	AG04449	skin:	fetal
15	chr12:10456885-10456935	GM06990	blood:	n/a
16	chr12:10456885-10456935	HepG2	liver:	n/a
17	chr12:10456885-10456935	NHBE	bronchial:	n/a
18	chr12:10456885-10456935	HCF	heart:	n/a
19	chr12:10456885-10456935	SAEC	small airway:	n/a
20	chr12:10456885-10456935	BJ	skin:	n/a
21	chr12:10456885-10456935	RPTEC	kidney:	n/a
22	chr12:10456885-10456935	K562	blood:	n/a
23	chr12:10456885-10456935	HIPEpiC	eye:	n/a
24	chr12:10456885-10456935	NT2-D1	testis:	n/a
25	chr12:10456885-10456935	HNPCEpiC	eye:	n/a
26	chr12:10456885-10456935	GM19239	blood:	n/a
27	chr12:10456885-10456935	HRCEpiC	kidney:	n/a
28	chr12:10456885-10456935	AG09319	gingival:	n/a
29	chr12:10456885-10456935	PFSK-1	brain:	n/a
30	chr12:10456885-10456935	SK-N-SH	brain:	n/a
31	chr12:10456885-10456935	BE2_C	brain:	n/a
32	chr12:10456885-10456935	AG04450	lung:	fetal
33	chr12:10456885-10456935	ProgFib	skin:	n/a
34	chr12:10456885-10456935	HPAEpiC	pulmonary alveolar:	n/a
35	chr12:10456885-10456935	GM12878	blood:	n/a
36	chr12:10456885-10456935	NB4	blood:	n/a
37	chr12:10456885-10456935	AG09309	skin:	n/a
38	chr12:10456885-10456935	T-47D	breast:	n/a
39	chr12:10456885-10456935	GM12891	blood:	n/a
40	chr12:10456885-10456935	Hela-S3	cervix:	n/a
41	chr12:10456885-10456935	H1-hESC	embryonic stem cell:	embryo
42	chr12:10456885-10456935	Caco-2	colon:	n/a
43	chr12:10456885-10456935	ovcar-3	ovarian:	n/a
44	chr12:10456885-10456935	AG10803	skin:	n/a
45	chr12:10456885-10456935	A549	lung:	n/a
46	chr12:10456885-10456935	U87	brain:	n/a
47	chr12:10456885-10456935	ECC-1	luminal epithelium:	n/a
48	chr12:10456885-10456935	SK-N-MC	brain:	n/a
49	chr12:10456885-10456935	HUVEC	blood vessel:	n/a
50	chr12:10456885-10456935	HCT-116	colon:	n/a

No data

Variant related genes	Relation type
KLRD1	TF binding region
KLRD1	CpG island

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11053738	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11053739	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11053740	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611333	0.89[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs12829155	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1600130	0.92[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2270238	0.90[GIH][hapmap]
rs2302489	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2537752	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2537781	0.96[CEU][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2617146	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759270	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3759272	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759273	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3867486	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3912117	0.92[CEU][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3927994	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4764341	0.80[TSI][hapmap]
rs61242400	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7135494	0.86[ASN][1000 genomes]
rs7301715	0.81[EUR][1000 genomes]
rs7313418	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs7316530	0.81[EUR][1000 genomes]
rs7961687	0.80[TSI][hapmap]
rs7964452	0.87[EUR][1000 genomes]
rs7970821	0.81[TSI][hapmap]
rs7972782	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832328	chr12:10398071-10620443	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv605	chr12:10448638-10494208	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv898759	chr12:10454556-10583365	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7314888	ATN1	cis	parietal	SCAN
rs7314888	NOP2	cis	cerebellum	SCAN
rs7314888	SLC2A3	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10453200-10461000	Weak transcription	Placenta	Placenta
2	chr12:10453400-10457000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr12:10453800-10457200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:10454200-10458000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:10454800-10474400	Weak transcription	Left Ventricle	heart
6	chr12:10456000-10457000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:10456200-10457200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:10456400-10457200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr12:10456400-10457800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:10456600-10457200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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