Variant report

Variant	rs752109
Chromosome Location	chr1:228247627-228247628
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228242970..228244835-chr1:228244981..228247673,2	MCF-7	breast:
2	chr1:228193180..228197909-chr1:228245616..228249822,4	MCF-7	breast:
3	chr1:228245943..228247915-chr1:228251913..228254649,3	K562	blood:
4	chr1:228246811..228249127-chr1:228257869..228259965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs15109	0.90[ASN][1000 genomes]
rs16848270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55686465	1.00[ASN][1000 genomes]
rs55904630	0.90[ASN][1000 genomes]
rs55923168	1.00[ASN][1000 genomes]
rs56003736	1.00[ASN][1000 genomes]
rs56029925	1.00[ASN][1000 genomes]
rs56080014	0.90[ASN][1000 genomes]
rs56154605	0.96[AFR][1000 genomes]
rs56285667	0.90[ASN][1000 genomes]
rs56377909	0.90[ASN][1000 genomes]
rs56831205	1.00[ASN][1000 genomes]
rs57446195	1.00[ASN][1000 genomes]
rs58045861	0.90[ASN][1000 genomes]
rs59478442	0.90[ASN][1000 genomes]
rs60245137	1.00[ASN][1000 genomes]
rs61230585	1.00[ASN][1000 genomes]
rs61401568	0.90[ASN][1000 genomes]
rs61737797	1.00[ASN][1000 genomes]
rs6675092	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140907	1.00[ASN][1000 genomes]
rs74140910	1.00[ASN][1000 genomes]
rs74140912	1.00[ASN][1000 genomes]
rs74140915	1.00[ASN][1000 genomes]
rs74140916	1.00[ASN][1000 genomes]
rs74140918	1.00[ASN][1000 genomes]
rs74140919	1.00[ASN][1000 genomes]
rs74140923	1.00[ASN][1000 genomes]
rs74140925	1.00[ASN][1000 genomes]
rs74140953	1.00[ASN][1000 genomes]
rs74140954	1.00[ASN][1000 genomes]
rs74140955	1.00[ASN][1000 genomes]
rs74140956	1.00[ASN][1000 genomes]
rs74140957	1.00[ASN][1000 genomes]
rs74140960	1.00[ASN][1000 genomes]
rs74140961	1.00[ASN][1000 genomes]
rs74140963	1.00[ASN][1000 genomes]
rs74140965	1.00[ASN][1000 genomes]
rs74140967	1.00[ASN][1000 genomes]
rs74140969	0.90[ASN][1000 genomes]
rs74140970	0.90[ASN][1000 genomes]
rs74140973	0.90[ASN][1000 genomes]
rs74140976	0.90[ASN][1000 genomes]
rs74140978	0.90[ASN][1000 genomes]
rs74140980	0.90[ASN][1000 genomes]
rs74140989	0.90[ASN][1000 genomes]
rs74140994	0.90[ASN][1000 genomes]
rs74140996	0.90[ASN][1000 genomes]
rs74141002	0.90[ASN][1000 genomes]
rs74142606	0.90[ASN][1000 genomes]
rs74142608	0.90[ASN][1000 genomes]
rs74142625	0.90[ASN][1000 genomes]
rs74142627	0.90[ASN][1000 genomes]
rs74142642	0.90[ASN][1000 genomes]
rs74142644	0.90[ASN][1000 genomes]
rs74142645	0.90[ASN][1000 genomes]
rs74142647	0.90[ASN][1000 genomes]
rs74143631	1.00[ASN][1000 genomes]
rs74143632	1.00[ASN][1000 genomes]
rs74143633	0.96[AFR][1000 genomes]
rs74143634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143636	1.00[ASN][1000 genomes]
rs74143637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143642	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143665	1.00[ASN][1000 genomes]
rs74143667	1.00[ASN][1000 genomes]
rs752108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	esv1814215	chr1:228231601-228259932	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
10	esv1844252	chr1:228231601-228259932	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv826964	chr1:228246802-228247654	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228246200-228248800	ZNF genes & repeats	Spleen	Spleen
2	chr1:228246400-228248200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:228246600-228248200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
4	chr1:228246600-228248200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
5	chr1:228246600-228248200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:228246600-228248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:228246600-228249000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:228246600-228249000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:228246600-228249000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:228246600-228249000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:228246800-228247800	Bivalent Enhancer	Fetal Heart	heart
12	chr1:228246800-228248000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
13	chr1:228246800-228248000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr1:228246800-228248000	Bivalent/Poised TSS	NHEK	skin
15	chr1:228246800-228248200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:228246800-228248600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
17	chr1:228246800-228249000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:228247000-228247800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:228247000-228247800	Bivalent Enhancer	Brain Hippocampus Middle	brain
20	chr1:228247000-228247800	Bivalent/Poised TSS	Colonic Mucosa	Colon
21	chr1:228247000-228247800	Bivalent Enhancer	Fetal Brain Male	brain
22	chr1:228247000-228247800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
23	chr1:228247000-228248000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
24	chr1:228247000-228248000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
25	chr1:228247000-228248200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
26	chr1:228247000-228248200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
27	chr1:228247000-228248200	Bivalent/Poised TSS	Esophagus	oesophagus
28	chr1:228247000-228248200	Bivalent/Poised TSS	Fetal Brain Female	brain
29	chr1:228247000-228248200	Bivalent Enhancer	Ovary	ovary
30	chr1:228247000-228248200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
31	chr1:228247000-228248400	Bivalent Enhancer	Fetal Thymus	thymus
32	chr1:228247000-228248400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr1:228247000-228248600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
34	chr1:228247000-228248600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr1:228247000-228248800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:228247000-228249000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr1:228247200-228247800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:228247200-228247800	Bivalent Enhancer	Fetal Stomach	stomach
39	chr1:228247200-228247800	Active TSS	Gastric	stomach
40	chr1:228247200-228247800	Bivalent/Poised TSS	A549	lung
41	chr1:228247200-228247800	Active TSS	K562	blood
42	chr1:228247200-228248000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
43	chr1:228247200-228248000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:228247200-228248000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:228247200-228248000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:228247200-228248200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:228247200-228248200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
48	chr1:228247200-228248200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
49	chr1:228247200-228248200	Active TSS	Pancreas	Pancrea
50	chr1:228247200-228248200	Active TSS	Right Atrium	heart

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