Variant report

Variant	rs6580660
Chromosome Location	chr12:48588112-48588113
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: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1018973	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1034762	0.81[CEU][hapmap]
rs10492080	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10783231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783233	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783237	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10783239	0.85[AMR][1000 genomes]
rs11168449	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168451	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11609399	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11612578	0.95[JPT][hapmap]
rs11613485	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12822085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1476608	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1489111	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs17122565	0.95[JPT][hapmap]
rs17122612	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs17122651	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1968071	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2013956	0.84[AMR][1000 genomes]
rs2054902	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2258342	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2409001	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2634679	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2634699	0.86[CHB][hapmap]
rs2732455	0.93[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2732458	0.81[CEU][hapmap]
rs2732477	0.93[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2732487	0.93[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3742074	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4075913	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4141065	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4760611	0.95[JPT][hapmap]
rs4760620	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4760623	0.85[AMR][1000 genomes]
rs4760683	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4760685	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4760692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580653	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6580656	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6580657	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726354	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294641	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7296913	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7305418	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312326	1.00[JPT][hapmap]
rs7313023	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315258	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7485057	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7485824	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs757556	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7953726	0.85[AMR][1000 genomes]
rs7963934	1.00[JPT][hapmap]
rs7969749	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7971668	1.00[JPT][hapmap]
rs879242	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs901962	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs901963	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs901964	0.86[CHB][hapmap];0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580660	ZNF641	cis	Whole Blood	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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