Variant report

Variant	rs10880089
Chromosome Location	chr12:41909244-41909245
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10459287	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506193	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785269	0.88[CEU][hapmap]
rs10880081	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10880082	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10880086	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880087	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880088	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880091	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880093	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880096	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10880097	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11180853	1.00[CHB][hapmap]
rs11180882	1.00[CHB][hapmap]
rs11180936	0.89[CEU][hapmap]
rs11180943	0.94[CEU][hapmap]
rs11180961	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11180979	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180980	1.00[JPT][hapmap]
rs11180981	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180988	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180989	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11180994	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12229610	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230775	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372586	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12427081	1.00[CHB][hapmap]
rs1350431	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379767	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1458153	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1458169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1551594	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1589983	1.00[CHB][hapmap]
rs17579291	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1902908	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608709	0.89[CEU][hapmap]
rs2733272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2733273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2733294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs285583	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285586	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285587	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3110189	0.89[CEU][hapmap]
rs3110389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768355	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs725527	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73130674	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974539	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv826349	chr12:41878846-41911495	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
2	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
3	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain
4	chr12:41904600-41915600	Weak transcription	Fetal Kidney	kidney
5	chr12:41905200-41916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:41907800-41915400	Weak transcription	Fetal Stomach	stomach
7	chr12:41908000-41915400	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:41908000-41915800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:41908200-41915400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:41908400-41909600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:41908400-41909600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:41908600-41909400	Weak transcription	Brain Substantia Nigra	brain
13	chr12:41908600-41909800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:41908600-41910000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:41908600-41915400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:41908800-41910000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:41908800-41915000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:41908800-41915600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:41909000-41909800	Weak transcription	Fetal Brain Male	brain

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