Variant report

Variant	rs12142487
Chromosome Location	chr1:171313275-171313276
allele	C/G
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	FOS	chr1:171313222-171313983	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr1:171313033-171313618	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr1:171313125-171313669	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr1:171313132-171313652	SK-N-SH	brain:	n/a	n/a
5	FOS	chr1:171313246-171313519	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr1:171312999-171313569	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr1:171313001-171313716	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000225704	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12065835	1.00[EUR][1000 genomes]
rs12117599	0.83[EUR][1000 genomes]
rs12119640	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12120784	1.00[EUR][1000 genomes]
rs12121703	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12122309	1.00[EUR][1000 genomes]
rs12130175	0.91[EUR][1000 genomes]
rs12131722	0.91[EUR][1000 genomes]
rs12138802	0.83[EUR][1000 genomes]
rs12142448	0.90[EUR][1000 genomes]
rs16864434	0.83[EUR][1000 genomes]
rs60349465	0.83[EUR][1000 genomes]
rs6667529	0.83[EUR][1000 genomes]
rs6674434	1.00[EUR][1000 genomes]
rs6674736	0.91[EUR][1000 genomes]
rs6675911	1.00[EUR][1000 genomes]
rs6699345	1.00[EUR][1000 genomes]
rs7516764	0.83[EUR][1000 genomes]
rs7518815	1.00[EUR][1000 genomes]
rs7525073	1.00[EUR][1000 genomes]
rs7545776	0.83[EUR][1000 genomes]
rs7548898	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1002423	chr1:171294384-171376936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv548188	chr1:171308832-171371998	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171284200-171313600	Weak transcription	Right Ventricle	heart
2	chr1:171284200-171313800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:171289400-171313400	Weak transcription	Fetal Lung	lung
4	chr1:171299800-171314200	Weak transcription	Aorta	Aorta
5	chr1:171305600-171315200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:171312400-171314400	Enhancers	Fetal Intestine Small	intestine
7	chr1:171312800-171315600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:171313000-171313400	Enhancers	Adipose Nuclei	Adipose
9	chr1:171313000-171313400	Enhancers	Right Atrium	heart
10	chr1:171313000-171313800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:171313000-171313800	Flanking Active TSS	Liver	Liver
12	chr1:171313000-171313800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:171313000-171314200	Enhancers	HepG2	liver
14	chr1:171313000-171314600	Enhancers	Fetal Intestine Large	intestine
15	chr1:171313200-171313600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:171313200-171313800	Active TSS	Duodenum Mucosa	Duodenum

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