Variant report

Variant	rs12044559
Chromosome Location	chr1:192609268-192609269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr1:192609042-192609549	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:192608262-192609442	Raji	blood:	n/a	n/a
3	TCF12	chr1:192608979-192609706	A549	lung:	n/a	n/a
4	JUND	chr1:192609021-192609459	GM12878	blood:	n/a	n/a
5	FOSL1	chr1:192609057-192609479	HCT-116	colon:	n/a	n/a
6	RELA	chr1:192608770-192609470	GM12878	blood:	n/a	n/a
7	FOS	chr1:192609202-192609404	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr1:192609080-192609579	A549	lung:	n/a	n/a
9	EBF1	chr1:192608776-192609468	GM12878	blood:	n/a	n/a
10	SP1	chr1:192609048-192609638	A549	lung:	n/a	n/a
11	EP300	chr1:192608968-192609692	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr1:192608988-192609671	SK-N-SH	brain:	n/a	chr1:192609246-192609254
13	BATF	chr1:192608704-192609522	GM12878	blood:	n/a	n/a
14	RUNX3	chr1:192609046-192609439	GM12878	blood:	n/a	n/a
15	GATA3	chr1:192608933-192609699	A549	lung:	n/a	chr1:192609246-192609254
16	EP300	chr1:192608836-192609492	GM12878	blood:	n/a	n/a
17	NFATC1	chr1:192609048-192609544	GM12878	blood:	n/a	n/a
18	GATA3	chr1:192608924-192609635	SK-N-SH	brain:	n/a	chr1:192609246-192609254
19	SP1	chr1:192609079-192609644	A549	lung:	n/a	n/a
20	TCF12	chr1:192608938-192609663	SK-N-SH	brain:	n/a	n/a
21	EP300	chr1:192608768-192609502	GM12878	blood:	n/a	n/a
22	MEF2A	chr1:192608913-192609526	SK-N-SH	brain:	n/a	chr1:192609200-192609221 chr1:192609204-192609219 chr1:192609206-192609217 chr1:192609200-192609221 chr1:192609200-192609221 chr1:192609205-192609219 chr1:192609207-192609216
23	FOSL2	chr1:192608931-192609663	A549	lung:	n/a	n/a
24	E2F4	chr1:192609165-192609539	MCF10A-Er-Src	breast:	n/a	n/a
25	BATF	chr1:192609075-192609486	GM12878	blood:	n/a	n/a
26	MAZ	chr1:192608730-192609822	GM12878	blood:	n/a	n/a
27	FOS	chr1:192609213-192609409	MCF10A-Er-Src	breast:	n/a	n/a
28	ATF3	chr1:192609110-192609424	HCT-116	colon:	n/a	n/a
29	NFIC	chr1:192608779-192609588	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr1:192608940-192609476	GM12878	blood:	n/a	n/a
31	MEF2C	chr1:192608847-192609512	GM12878	blood:	n/a	chr1:192609200-192609221 chr1:192609204-192609219 chr1:192609206-192609217 chr1:192609200-192609221 chr1:192609200-192609221 chr1:192609203-192609218 chr1:192609205-192609219 chr1:192609207-192609216
32	FOS	chr1:192609206-192609406	MCF10A-Er-Src	breast:	n/a	n/a
33	BHLHE40	chr1:192608752-192609508	GM12878	blood:	n/a	n/a
34	JUND	chr1:192609053-192609676	HCT-116	colon:	n/a	n/a
35	REST	chr1:192609246-192609387	GM12878	blood:	n/a	n/a
36	FOS	chr1:192609214-192609403	MCF10A-Er-Src	breast:	n/a	n/a
37	FOSL2	chr1:192609109-192609459	A549	lung:	n/a	n/a
38	ARID3A	chr1:192609243-192609525	HepG2	liver:	n/a	n/a
39	CEBPB	chr1:192609091-192609619	HCT-116	colon:	n/a	n/a
40	MYC	chr1:192609264-192609385	MCF10A-Er-Src	breast:	n/a	n/a
41	ATF2	chr1:192608713-192609547	GM12878	blood:	n/a	n/a
42	NFIC	chr1:192608725-192609573	GM12878	blood:	n/a	n/a
43	FOXM1	chr1:192609018-192609555	GM12878	blood:	n/a	n/a
44	CEBPB	chr1:192609195-192609482	A549	lung:	n/a	n/a
45	FOSL1	chr1:192608996-192609595	HCT-116	colon:	n/a	n/a
46	SP1	chr1:192608960-192609646	HCT-116	colon:	n/a	n/a
47	CEBPB	chr1:192608983-192609650	HCT-116	colon:	n/a	n/a
48	ATF2	chr1:192608881-192609507	GM12878	blood:	n/a	n/a
49	MEF2A	chr1:192608861-192609461	GM12878	blood:	n/a	chr1:192609200-192609221 chr1:192609204-192609219 chr1:192609206-192609217 chr1:192609200-192609221 chr1:192609200-192609221 chr1:192609205-192609219 chr1:192609207-192609216
50	CEBPB	chr1:192609143-192609518	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:192607291..192610228-chr1:192623335..192626008,2	K562	blood:

Variant related genes	Relation type
RGS13	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10127997	0.98[EUR][1000 genomes]
rs10801138	0.91[CHB][hapmap];0.88[MEX][hapmap]
rs12759003	0.98[EUR][1000 genomes]
rs3795617	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3884536	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4233424	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4319308	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59105666	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658382	0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[MEX][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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv467005	chr1:192549912-192625360	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv548659	chr1:192549912-192625360	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv548660	chr1:192609268-192945348	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12044559	RGS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192600200-192620400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:192607600-192609400	Enhancers	Fetal Intestine Small	intestine
3	chr1:192608000-192610800	Enhancers	Fetal Lung	lung
4	chr1:192608200-192609600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:192608200-192609600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:192608200-192609600	Enhancers	Ovary	ovary
7	chr1:192608200-192609800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:192608200-192609800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:192608200-192610000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:192608200-192611000	Enhancers	Fetal Intestine Large	intestine
11	chr1:192608400-192609400	Bivalent Enhancer	Primary B cells from cord blood	blood
12	chr1:192608400-192609400	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:192608400-192609800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:192608400-192610000	Enhancers	GM12878-XiMat	blood
15	chr1:192608600-192609800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:192608600-192610200	Enhancers	A549	lung
17	chr1:192608800-192609400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:192608800-192609400	Enhancers	Duodenum Mucosa	Duodenum
19	chr1:192608800-192609600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:192608800-192609600	Enhancers	HSMMtube	muscle
21	chr1:192608800-192609600	Enhancers	NH-A	brain
22	chr1:192608800-192609800	Enhancers	Osteobl	bone
23	chr1:192608800-192610200	Enhancers	Hela-S3	cervix
24	chr1:192609000-192609400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:192609000-192609400	Enhancers	NHLF	lung
26	chr1:192609200-192609400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:192609200-192609600	Enhancers	Fetal Heart	heart
28	chr1:192609200-192609600	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links