Variant report

Variant	rs12138092
Chromosome Location	chr1:227513677-227513678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227511186..227513689-chr1:227514220..227516640,3	K562	blood:
2	chr1:227506088..227508299-chr1:227513676..227515983,2	MCF-7	breast:
3	chr1:227512596..227514265-chr1:227521863..227524248,2	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10916112	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916113	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916116	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916125	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11576239	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11584325	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11585910	0.96[AMR][1000 genomes]
rs12119153	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12123597	0.81[AMR][1000 genomes]
rs12128174	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12131061	0.89[AMR][1000 genomes]
rs12131459	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12131933	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12133230	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12133633	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12138364	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12138383	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12138664	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12144205	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12746316	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12754677	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12755770	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1513607	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1513613	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17613235	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2063661	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28648445	0.96[AMR][1000 genomes]
rs34113967	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34702208	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34897490	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35160496	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35952573	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4308948	0.89[AMR][1000 genomes]
rs61834323	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61834324	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61834326	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61834590	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61834625	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834626	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6660168	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6675408	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6675572	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6678714	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6697583	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7512871	0.81[AMR][1000 genomes]
rs7518813	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7523759	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543419	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7548118	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227507000-227515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:227509400-227516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:227510400-227516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:227511600-227515600	Weak transcription	Liver	Liver
6	chr1:227511600-227518000	Weak transcription	K562	blood
7	chr1:227512000-227516400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:227512000-227523200	Weak transcription	Stomach Mucosa	stomach
9	chr1:227513200-227516200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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