Variant report

Variant	rs74142625
Chromosome Location	chr1:228364568-228364569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228362275..228366557-chr1:228367502..228371326,4	MCF-7	breast:
2	chr1:228301175..228302855-chr1:228364193..228366742,2	K562	blood:
3	chr1:228362968..228364679-chr1:228382995..228385252,2	K562	blood:
4	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
5	chr1:228359558..228361063-chr1:228363819..228365618,2	MCF-7	breast:
6	chr1:228362964..228365740-chr1:228389422..228392205,2	K562	blood:
7	chr1:228352925..228354845-chr1:228364134..228367346,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

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]
rs74142627	1.00[ASN][1000 genomes]
rs74142631	1.00[AFR][1000 genomes]
rs74142641	1.00[AFR][1000 genomes]
rs74142642	1.00[ASN][1000 genomes]
rs74142643	1.00[AFR][1000 genomes]
rs74142644	1.00[ASN][1000 genomes]
rs74142645	1.00[ASN][1000 genomes]
rs74142647	1.00[ASN][1000 genomes]
rs74142649	1.00[AFR][1000 genomes]
rs74142654	1.00[AFR][1000 genomes]
rs74142656	1.00[AFR][1000 genomes]
rs74142660	1.00[AFR][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:16 , 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	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
5	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
6	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
7	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
8	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
9	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
10	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
12	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
13	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
14	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
15	esv1806558	chr1:228358977-228365154	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228370400	Weak transcription	Right Atrium	heart
3	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
5	chr1:228354800-228364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:228354800-228365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:228354800-228366400	Weak transcription	Liver	Liver
8	chr1:228354800-228367000	Weak transcription	Osteobl	bone
9	chr1:228354800-228370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:228354800-228371200	Weak transcription	HSMMtube	muscle
11	chr1:228354800-228373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:228355000-228364600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:228355000-228364800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:228355000-228364800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:228355000-228370600	Weak transcription	HepG2	liver
16	chr1:228355000-228372400	Weak transcription	Stomach Mucosa	stomach
17	chr1:228355000-228373200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:228355000-228373200	Weak transcription	Hela-S3	cervix
19	chr1:228361200-228366400	Genic enhancers	Fetal Stomach	stomach
20	chr1:228361800-228364600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:228361800-228365800	Genic enhancers	Spleen	Spleen
22	chr1:228362200-228364800	Strong transcription	Brain Germinal Matrix	brain
23	chr1:228362200-228365000	Strong transcription	Pancreas	Pancrea
24	chr1:228362400-228364800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:228362400-228364800	Strong transcription	Ovary	ovary
26	chr1:228362400-228365000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:228362400-228365000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:228362400-228365000	Strong transcription	Gastric	stomach
29	chr1:228362600-228364600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:228362600-228364600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:228362600-228364800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:228362600-228365000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:228362600-228365200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:228362600-228365200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:228362600-228365400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:228362600-228365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:228362600-228365800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:228362600-228365800	Strong transcription	Fetal Brain Female	brain
39	chr1:228362600-228368600	Weak transcription	Psoas Muscle	Psoas
40	chr1:228362800-228364600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:228362800-228364800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:228362800-228364800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:228362800-228364800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:228362800-228365000	Strong transcription	Fetal Intestine Large	intestine
45	chr1:228362800-228365200	Strong transcription	Thymus	Thymus
46	chr1:228362800-228365600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:228362800-228365600	Weak transcription	K562	blood
48	chr1:228362800-228366600	Strong transcription	Primary T cells from cord blood	blood
49	chr1:228363200-228364600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:228363200-228364800	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links