Variant report

Variant	rs28493579
Chromosome Location	chr2:152154550-152154551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152153051..152154778-chr2:152157552..152159537,2	K562	blood:
2	chr2:152153051..152155912-chr2:152157552..152160474,3	K562	blood:
3	chr2:152144796..152146879-chr2:152152335..152156277,3	MCF-7	breast:
4	chr2:152145323..152148173-chr2:152152991..152155246,2	K562	blood:
5	chr2:152145273..152146858-chr2:152154476..152156576,2	MCF-7	breast:
6	chr2:152154122..152156029-chr2:152157946..152160743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123609	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10173695	1.00[AMR][1000 genomes]
rs10179626	1.00[AMR][1000 genomes]
rs10180428	1.00[AMR][1000 genomes]
rs10190464	1.00[AMR][1000 genomes]
rs10191465	1.00[AMR][1000 genomes]
rs10193304	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10195365	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10201647	1.00[AMR][1000 genomes]
rs10202368	1.00[AMR][1000 genomes]
rs10203338	1.00[AMR][1000 genomes]
rs10205770	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205976	1.00[AMR][1000 genomes]
rs10206584	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10210009	1.00[AMR][1000 genomes]
rs12328054	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12328381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12328560	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383657	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13385932	1.00[AMR][1000 genomes]
rs13387765	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13389056	1.00[AMR][1000 genomes]
rs13389461	1.00[AMR][1000 genomes]
rs13390792	1.00[AMR][1000 genomes]
rs13394505	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13395395	1.00[AMR][1000 genomes]
rs13395749	1.00[AMR][1000 genomes]
rs13399299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13408667	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13408684	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411396	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13412493	1.00[AMR][1000 genomes]
rs13412781	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13417120	1.00[AMR][1000 genomes]
rs13418019	1.00[AMR][1000 genomes]
rs13418799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13420365	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13423692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13426840	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2303341	1.00[AMR][1000 genomes]
rs28445248	1.00[AMR][1000 genomes]
rs28529741	1.00[AMR][1000 genomes]
rs3771899	1.00[AMR][1000 genomes]
rs56801020	1.00[AMR][1000 genomes]
rs59089077	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59356545	1.00[AMR][1000 genomes]
rs6719796	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6724871	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6747290	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9989812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
6	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152149400-152158800	Weak transcription	K562	blood
2	chr2:152152600-152158600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:152153800-152155400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:152153800-152155400	Enhancers	HUVEC	blood vessel
5	chr2:152154000-152154800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:152154000-152155200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr2:152154000-152155400	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:152154200-152154600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr2:152154200-152154600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr2:152154200-152155200	Enhancers	Primary B cells from cord blood	blood
11	chr2:152154200-152155200	Enhancers	Primary hematopoietic stem cells	blood
12	chr2:152154200-152155200	Enhancers	GM12878-XiMat	blood
13	chr2:152154200-152155800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr2:152154400-152154800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:152154400-152155000	Enhancers	Brain Angular Gyrus	brain

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