Variant report

Variant	rs74142645
Chromosome Location	chr1:228393260-228393261
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228390590-228393912	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:228390067-228395890	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:228393247-228394243	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228277955..228280609-chr1:228391236..228393564,2	K562	blood:
2	chr1:228392712..228394429-chr1:228455538..228457538,2	K562	blood:
3	chr1:228392725..228394871-chr1:228701724..228704719,2	K562	blood:
4	chr1:228382588..228385276-chr1:228392275..228394385,3	MCF-7	breast:
5	chr1:228392443..228395548-chr1:228398360..228402800,4	MCF-7	breast:

No data

Variant related genes	Relation type
OBSCN	TF binding region
ENSG00000162913	Chromatin interaction
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs15109	1.00[ASN][1000 genomes]
rs16848270	0.90[ASN][1000 genomes]
rs55686465	0.90[ASN][1000 genomes]
rs55904630	1.00[ASN][1000 genomes]
rs55923168	0.90[ASN][1000 genomes]
rs56003736	0.90[ASN][1000 genomes]
rs56029925	0.90[ASN][1000 genomes]
rs56080014	1.00[ASN][1000 genomes]
rs56285667	1.00[ASN][1000 genomes]
rs56377909	1.00[ASN][1000 genomes]
rs56831205	0.90[ASN][1000 genomes]
rs57446195	0.90[ASN][1000 genomes]
rs58045861	1.00[ASN][1000 genomes]
rs59478442	1.00[ASN][1000 genomes]
rs60245137	0.90[ASN][1000 genomes]
rs61230585	0.90[ASN][1000 genomes]
rs61401568	1.00[ASN][1000 genomes]
rs61737797	0.90[ASN][1000 genomes]
rs74140907	0.90[ASN][1000 genomes]
rs74140910	0.90[ASN][1000 genomes]
rs74140912	0.90[ASN][1000 genomes]
rs74140915	0.90[ASN][1000 genomes]
rs74140916	0.90[ASN][1000 genomes]
rs74140918	0.90[ASN][1000 genomes]
rs74140919	0.90[ASN][1000 genomes]
rs74140923	0.90[ASN][1000 genomes]
rs74140925	0.90[ASN][1000 genomes]
rs74140953	0.90[ASN][1000 genomes]
rs74140954	0.90[ASN][1000 genomes]
rs74140955	0.90[ASN][1000 genomes]
rs74140956	0.90[ASN][1000 genomes]
rs74140957	0.90[ASN][1000 genomes]
rs74140960	0.90[ASN][1000 genomes]
rs74140961	0.90[ASN][1000 genomes]
rs74140963	0.90[ASN][1000 genomes]
rs74140965	0.90[ASN][1000 genomes]
rs74140967	0.90[ASN][1000 genomes]
rs74140969	0.81[ASN][1000 genomes]
rs74140970	1.00[ASN][1000 genomes]
rs74140973	1.00[ASN][1000 genomes]
rs74140976	1.00[ASN][1000 genomes]
rs74140978	1.00[ASN][1000 genomes]
rs74140980	1.00[ASN][1000 genomes]
rs74140989	1.00[ASN][1000 genomes]
rs74140994	1.00[ASN][1000 genomes]
rs74140996	1.00[ASN][1000 genomes]
rs74141002	1.00[ASN][1000 genomes]
rs74142606	1.00[ASN][1000 genomes]
rs74142608	1.00[ASN][1000 genomes]
rs74142625	1.00[ASN][1000 genomes]
rs74142627	1.00[ASN][1000 genomes]
rs74142642	1.00[ASN][1000 genomes]
rs74142644	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:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228366800-228393400	Weak transcription	Right Ventricle	heart
2	chr1:228373800-228394000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:228383200-228394600	Weak transcription	Fetal Brain Male	brain
4	chr1:228385600-228393400	Weak transcription	Left Ventricle	heart
5	chr1:228387400-228393600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:228388000-228393600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:228388400-228393800	Weak transcription	Liver	Liver
8	chr1:228392200-228394400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:228392200-228395600	Enhancers	Fetal Muscle Leg	muscle
10	chr1:228392400-228393800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:228392600-228395000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:228392800-228393800	Enhancers	HSMMtube	muscle
13	chr1:228392800-228394000	Weak transcription	Brain Germinal Matrix	brain
14	chr1:228392800-228394400	Enhancers	Brain Anterior Caudate	brain
15	chr1:228392800-228395200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr1:228392800-228396200	Enhancers	Spleen	Spleen
17	chr1:228392800-228396400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:228392800-228396400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:228393000-228394600	Enhancers	Fetal Lung	lung
20	chr1:228393200-228394800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:228393200-228395200	Enhancers	Fetal Heart	heart
22	chr1:228393200-228395600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links