Variant report

Variant	rs74140980
Chromosome Location	chr1:228308398-228308399
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228296490..228298272-chr1:228307329..228308840,2	K562	blood:
2	chr1:228302676..228304772-chr1:228307027..228309907,2	MCF-7	breast:
3	chr1:228305346..228307341-chr1:228307911..228310651,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GUK1-2	chr1:228306596-228311865	NONHSAT009977

Variant related genes	Relation type
ENSG00000224566	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10127654	1.00[AMR][1000 genomes]
rs11541554	1.00[AMR][1000 genomes]
rs15109	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16848270	0.90[ASN][1000 genomes]
rs2231717	1.00[AMR][1000 genomes]
rs3754359	0.85[AFR][1000 genomes]
rs55662277	1.00[AMR][1000 genomes]
rs55686465	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55904630	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55923168	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56003736	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56029925	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs56080014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56137152	1.00[AMR][1000 genomes]
rs56280722	1.00[AMR][1000 genomes]
rs56285667	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56377909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56386805	1.00[AMR][1000 genomes]
rs56410225	1.00[AMR][1000 genomes]
rs56831205	0.90[ASN][1000 genomes]
rs57446195	0.90[ASN][1000 genomes]
rs58045861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59460700	1.00[AMR][1000 genomes]
rs59478442	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60245137	0.90[ASN][1000 genomes]
rs60628313	1.00[AMR][1000 genomes]
rs61100243	1.00[AMR][1000 genomes]
rs61230585	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61401568	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61737797	0.90[ASN][1000 genomes]
rs74140905	0.85[AFR][1000 genomes]
rs74140907	0.90[ASN][1000 genomes]
rs74140910	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140912	0.90[ASN][1000 genomes]
rs74140915	0.90[ASN][1000 genomes]
rs74140916	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140918	0.90[ASN][1000 genomes]
rs74140919	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140925	0.90[ASN][1000 genomes]
rs74140953	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140954	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140956	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140957	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140960	0.90[ASN][1000 genomes]
rs74140961	0.90[ASN][1000 genomes]
rs74140962	0.85[AFR][1000 genomes]
rs74140963	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140965	0.90[ASN][1000 genomes]
rs74140967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74140968	0.85[AFR][1000 genomes]
rs74140969	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs74140970	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140985	0.93[AFR][1000 genomes]
rs74140986	1.00[AMR][1000 genomes]
rs74140987	1.00[AMR][1000 genomes]
rs74140988	1.00[AMR][1000 genomes]
rs74140989	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140990	1.00[AMR][1000 genomes]
rs74140994	1.00[ASN][1000 genomes]
rs74140996	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140999	1.00[AMR][1000 genomes]
rs74141000	1.00[AMR][1000 genomes]
rs74141002	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74142604	1.00[AMR][1000 genomes]
rs74142605	1.00[AMR][1000 genomes]
rs74142606	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74142608	1.00[ASN][1000 genomes]
rs74142610	1.00[AMR][1000 genomes]
rs74142611	1.00[AMR][1000 genomes]
rs74142613	1.00[AMR][1000 genomes]
rs74142618	1.00[AMR][1000 genomes]
rs74142619	1.00[AMR][1000 genomes]
rs74142622	1.00[AMR][1000 genomes]
rs74142625	1.00[ASN][1000 genomes]
rs74142626	1.00[AMR][1000 genomes]
rs74142627	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74142629	1.00[AMR][1000 genomes]
rs74142630	1.00[AMR][1000 genomes]
rs74142642	1.00[ASN][1000 genomes]
rs74142644	1.00[ASN][1000 genomes]
rs74142645	1.00[ASN][1000 genomes]
rs74142647	1.00[ASN][1000 genomes]
rs74143631	0.90[ASN][1000 genomes]
rs74143632	0.90[ASN][1000 genomes]
rs74143634	0.90[ASN][1000 genomes]
rs74143635	0.90[ASN][1000 genomes]
rs74143636	0.90[ASN][1000 genomes]
rs74143637	0.90[ASN][1000 genomes]
rs74143638	0.90[ASN][1000 genomes]
rs74143640	0.90[ASN][1000 genomes]
rs74143641	0.90[ASN][1000 genomes]
rs74143642	0.90[ASN][1000 genomes]
rs74143662	0.90[ASN][1000 genomes]
rs74143665	0.90[ASN][1000 genomes]
rs74143667	0.90[ASN][1000 genomes]
rs752108	0.90[ASN][1000 genomes]
rs752109	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS 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	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
6	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
9	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
10	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228306400-228309800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:228307200-228309000	Enhancers	HSMMtube	muscle
3	chr1:228307200-228309200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:228307400-228308400	Enhancers	NHDF-Ad	bronchial
5	chr1:228307400-228308800	Enhancers	HMEC	breast
6	chr1:228307600-228308800	Flanking Active TSS	NHEK	skin
7	chr1:228307800-228308800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:228308000-228308800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:228308200-228308600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:228308200-228308600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:228308200-228309200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:228308200-228309400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links