Variant report

Variant	rs12022825
Chromosome Location	chr1:241990619-241990620
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	POLR2A	chr1:241990497-241990955	H1-neurons	neurons:	n/a	n/a
2	GATA2	chr1:241990455-241990851	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr1:241990443-241990897	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241988599..241991404-chr1:241995097..241997500,3	K562	blood:
2	chr1:241983775..241986188-chr1:241988893..241991233,2	K562	blood:
3	chr1:241986331..241988478-chr1:241989134..241991324,3	K562	blood:

Variant related genes	Relation type
ENSG00000229022	TF binding region
ENSG00000229022	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1017018	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10737868	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs10802990	0.85[JPT][hapmap]
rs10926564	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs10926569	0.95[JPT][hapmap]
rs12038477	0.90[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042255	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1418764	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1891566	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4129118	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4428871	0.85[ASN][1000 genomes]
rs4658661	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs55865277	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59836392	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6413961	0.91[JPT][hapmap]
rs6429301	0.86[JPT][hapmap]
rs6429312	0.83[ASN][1000 genomes]
rs6429313	0.85[ASN][1000 genomes]
rs6429314	0.86[ASN][1000 genomes]
rs6660811	0.85[JPT][hapmap]
rs6666953	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6669036	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6669629	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6680142	0.85[JPT][hapmap]
rs6695661	0.85[JPT][hapmap]
rs6696527	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs72755248	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72755251	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418198	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7418599	0.85[JPT][hapmap]
rs7418764	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7530797	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7533622	0.86[ASN][1000 genomes]
rs7551270	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9428515	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9428516	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9428520	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9428521	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9428524	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9428525	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9428527	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9428529	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9428891	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9428892	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9428893	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9428894	0.90[CEU][hapmap];0.92[AMR][1000 genomes]
rs9428898	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9428899	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9428900	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9428901	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9428902	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs952084	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv948409	chr1:241830086-242489705	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv528015	chr1:241865219-242070731	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008300	chr1:241886514-242171611	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2762521	chr1:241891040-242074222	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv873373	chr1:241939069-242027500	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv873374	chr1:241975147-242097624	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241981200-241992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:241985000-241992000	Weak transcription	Osteobl	bone
3	chr1:241985600-241990800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:241985600-241991800	Weak transcription	NHLF	lung
5	chr1:241985600-241992000	Weak transcription	NHDF-Ad	bronchial
6	chr1:241985800-241991800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:241987800-241992000	Weak transcription	K562	blood
8	chr1:241989000-241991800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:241989000-241992000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:241989000-241992400	Enhancers	Fetal Brain Male	brain
11	chr1:241989200-241991000	Weak transcription	Left Ventricle	heart
12	chr1:241989200-241992000	Weak transcription	HSMM	muscle
13	chr1:241989600-241991600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:241989600-241992600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:241989800-241990800	Weak transcription	Aorta	Aorta
16	chr1:241990600-241990800	Enhancers	Right Ventricle	heart
17	chr1:241990600-241991000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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