Variant report

Variant	rs12023196
Chromosome Location	chr1:152783724-152783725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:152783549-152783867	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:152783561-152783798	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF274	chr1:152783535-152783729	NT2-D1	testis:	n/a	n/a
4	FOS	chr1:152783588-152783913	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:152783582-152783867	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:152783559-152783858	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr1:152783588-152783840	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr1:152783505-152783891	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr1:152783263-152783886	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:152783583-152783839	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr1:152783582-152783854	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:152783674-152783724	MCF-7	breast:	n/a
2	chr1:152783674-152783724	IMR90	lung:	fetal
3	chr1:152783674-152783724	NH-A	brain:	n/a
4	chr1:152783674-152783724	GM12878	blood:	n/a
5	chr1:152783674-152783724	HRPEpiC	eye:	n/a
6	chr1:152783674-152783724	HMEC	breast:	n/a
7	chr1:152783674-152783724	PFSK-1	brain:	n/a
8	chr1:152783674-152783724	Jurkat	blood:	n/a
9	chr1:152783674-152783724	NB4	blood:	n/a
10	chr1:152783674-152783724	RPTEC	kidney:	n/a
11	chr1:152783674-152783724	HRCEpiC	kidney:	n/a
12	chr1:152783674-152783724	K562	blood:	n/a
13	chr1:152783674-152783724	AoSMC	blood vessel:	n/a
14	chr1:152783674-152783724	AG04449	skin:	fetal
15	chr1:152783674-152783724	HCF	heart:	n/a
16	chr1:152783674-152783724	NT2-D1	testis:	n/a
17	chr1:152783674-152783724	ProgFib	skin:	n/a
18	chr1:152783674-152783724	HPAEpiC	pulmonary alveolar:	n/a
19	chr1:152783674-152783724	HCM	heart:	n/a
20	chr1:152783674-152783724	ovcar-3	ovarian:	n/a
21	chr1:152783674-152783724	HEK293	kidney:	embryo
22	chr1:152783674-152783724	AG04450	lung:	fetal
23	chr1:152783674-152783724	CMK	blood:	n/a
24	chr1:152783674-152783724	MCF10A-Er-Src	breast:	n/a
25	chr1:152783674-152783724	T-47D	breast:	n/a
26	chr1:152783674-152783724	AG09319	gingival:	n/a
27	chr1:152783674-152783724	GM12891	blood:	n/a
28	chr1:152783674-152783724	HUVEC	blood vessel:	n/a
29	chr1:152783674-152783724	LNCaP	prostate:	n/a
30	chr1:152783674-152783724	GM19239	blood:	n/a
31	chr1:152783674-152783724	GM06990	blood:	n/a
32	chr1:152783674-152783724	AG10803	skin:	n/a
33	chr1:152783674-152783724	BE2_C	brain:	n/a
34	chr1:152783674-152783724	HL-60	blood:	n/a
35	chr1:152783674-152783724	SKMC	muscle:	n/a
36	chr1:152783674-152783724	Hela-S3	cervix:	n/a
37	chr1:152783674-152783724	GM12892	blood:	n/a
38	chr1:152783674-152783724	HRE	kidney:	n/a
39	chr1:152783674-152783724	U87	brain:	n/a
40	chr1:152783674-152783724	NHDF-neo	bronchial:	n/a
41	chr1:152783674-152783724	Hepatocyte	liver:	n/a
42	chr1:152783674-152783724	H1-hESC	embryonic stem cell:	embryo
43	chr1:152783674-152783724	Caco-2	colon:	n/a
44	chr1:152783674-152783724	ECC-1	luminal epithelium:	n/a
45	chr1:152783674-152783724	HNPCEpiC	eye:	n/a
46	chr1:152783674-152783724	SK-N-MC	brain:	n/a
47	chr1:152783674-152783724	HepG2	liver:	n/a
48	chr1:152783674-152783724	SAEC	small airway:	n/a
49	chr1:152783674-152783724	BJ	skin:	n/a
50	chr1:152783674-152783724	PrEC	prostate:	n/a

No data

Variant related genes	Relation type
LCE1C	TF binding region
LCE1B	TF binding region
LCE1B	CpG island
LCE1C	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12025125	0.87[CHD][hapmap]
rs6701216	0.87[CHD][hapmap]
rs7536191	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs877656	0.87[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv947325	chr1:152670204-152793272	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	nsv508615	chr1:152724155-152787503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv1799675	chr1:152759643-152785456	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1010346	chr1:152761911-152787707	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1012943	chr1:152762750-152787707	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv1009885	chr1:152762750-152851273	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12023196	RPTN	cis	cerebellum	SCAN
rs12023196	LCE1E	cis	lymphoblastoid	seeQTL
rs12023196	ADAMTSL4	cis	parietal	SCAN
rs12023196	ACP6	cis	cerebellum	SCAN
rs12023196	SCNM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152783000-152784200	Enhancers	NHEK	skin
2	chr1:152783200-152784400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:152783200-152784400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:152783400-152784200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152783400-152784400	Enhancers	HMEC	breast
6	chr1:152783600-152784000	Active TSS	Gastric	stomach
7	chr1:152783600-152784200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:152783600-152784200	Enhancers	Esophagus	oesophagus

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