Variant report

Variant	rs6580659
Chromosome Location	chr12:48588035-48588036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48587647..48589983-chr12:48590622..48592534,2	K562	blood:
2	chr12:48577879..48579746-chr12:48586715..48588244,2	K562	blood:
3	chr12:48583505..48585378-chr12:48585975..48588176,2	MCF-7	breast:
4	chr12:48582939..48585251-chr12:48585602..48588583,3	K562	blood:
5	chr12:48582939..48584871-chr12:48586838..48589561,2	K562	blood:

Variant related genes	Relation type
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10082861	1.00[JPT][hapmap]
rs1021313	0.81[ASN][1000 genomes]
rs10219623	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10437919	0.81[ASN][1000 genomes]
rs10437920	0.81[ASN][1000 genomes]
rs10467101	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10783234	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875724	0.92[JPT][hapmap]
rs10875725	1.00[JPT][hapmap]
rs10875732	1.00[JPT][hapmap]
rs10875745	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10875746	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10875750	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10875756	0.82[ASN][1000 genomes]
rs10875762	0.90[ASN][1000 genomes]
rs10875764	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875767	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10875768	0.86[ASN][1000 genomes]
rs10875769	0.86[ASN][1000 genomes]
rs10875770	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10875772	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875777	0.81[ASN][1000 genomes]
rs10875778	0.81[ASN][1000 genomes]
rs10875779	0.81[ASN][1000 genomes]
rs10875792	0.83[JPT][hapmap]
rs10875793	0.91[JPT][hapmap]
rs11168357	0.92[JPT][hapmap]
rs11168369	1.00[JPT][hapmap]
rs11168371	1.00[JPT][hapmap]
rs11168403	1.00[JPT][hapmap]
rs11168413	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11168414	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11168418	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11168420	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11168421	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11168425	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11168427	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11168433	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168459	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168487	0.81[ASN][1000 genomes]
rs11168516	0.85[JPT][hapmap]
rs11558768	0.89[ASN][1000 genomes]
rs12297470	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12304476	1.00[JPT][hapmap]
rs12305182	0.92[JPT][hapmap]
rs12305511	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12305647	0.92[ASN][1000 genomes]
rs12306451	1.00[JPT][hapmap]
rs12310813	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12312134	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs12317751	0.81[ASN][1000 genomes]
rs1471997	0.84[JPT][hapmap]
rs17122666	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17122812	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1859445	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2012773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054903	0.85[JPT][hapmap]
rs2079295	0.92[JPT][hapmap]
rs2107638	1.00[JPT][hapmap]
rs2228500	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2269933	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2269935	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2269936	1.00[JPT][hapmap]
rs2279464	0.85[JPT][hapmap]
rs2634675	0.85[JPT][hapmap]
rs2732439	0.85[JPT][hapmap]
rs2732465	0.85[JPT][hapmap]
rs3185921	0.85[JPT][hapmap]
rs3751273	0.85[JPT][hapmap]
rs3782910	1.00[JPT][hapmap]
rs4760609	0.92[JPT][hapmap]
rs4760619	1.00[JPT][hapmap]
rs4760622	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4760681	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4760687	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4760689	0.82[ASN][1000 genomes]
rs4760690	0.82[ASN][1000 genomes]
rs4760695	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4760696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760697	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760699	0.83[ASN][1000 genomes]
rs61940962	0.84[ASN][1000 genomes]
rs61941003	0.81[ASN][1000 genomes]
rs61941006	0.81[ASN][1000 genomes]
rs7135779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs716553	0.81[ASN][1000 genomes]
rs719008	0.92[JPT][hapmap]
rs725454	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7299135	0.92[JPT][hapmap]
rs7299271	0.92[JPT][hapmap]
rs7303055	0.81[ASN][1000 genomes]
rs7486008	0.81[ASN][1000 genomes]
rs7486424	1.00[JPT][hapmap]
rs8804	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs886588	1.00[JPT][hapmap]
rs9634261	0.85[JPT][hapmap]
rs989144	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6580659	ZNF641	cis	Muscle Skeletal	GTEx
rs6580659	ZNF641	cis	Whole Blood	GTEx
rs6580659	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48580000-48591000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:48583000-48590200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:48583800-48588200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48585400-48590800	Weak transcription	HMEC	breast
5	chr12:48585800-48589800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:48585800-48591400	Weak transcription	Esophagus	oesophagus
7	chr12:48587400-48589200	Enhancers	Hela-S3	cervix
8	chr12:48587400-48590600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:48587400-48590800	Weak transcription	NHEK	skin
10	chr12:48587600-48590800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:48588000-48588200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:48588000-48588400	Weak transcription	A549	lung
13	chr12:48588000-48588600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:48588000-48589400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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