Variant report

Variant	rs10880090
Chromosome Location	chr12:41914939-41914940
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10219633	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs10506194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10506196	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs10785234	0.89[CHB][hapmap]
rs10880037	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880068	0.89[CHB][hapmap]
rs10880069	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880070	0.89[CHB][hapmap]
rs10880080	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs10880083	0.89[CHB][hapmap]
rs10880084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880085	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10880097	0.90[JPT][hapmap]
rs10880101	0.90[JPT][hapmap]
rs10880102	0.90[JPT][hapmap]
rs11180830	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180833	0.88[CHB][hapmap]
rs11180840	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180841	0.89[CHB][hapmap]
rs11180844	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180845	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180849	0.88[CHB][hapmap]
rs11180852	0.86[CHB][hapmap]
rs11180860	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180868	0.88[CHB][hapmap]
rs11180873	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180874	0.88[CHB][hapmap]
rs11180875	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180879	0.89[CHB][hapmap]
rs11180883	0.89[CHB][hapmap]
rs11180886	0.89[CHB][hapmap]
rs11180903	0.89[CHB][hapmap]
rs11180913	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180915	0.88[CHB][hapmap]
rs11180917	0.89[CHB][hapmap]
rs11180921	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180922	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180928	0.89[CHB][hapmap]
rs11180932	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180935	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs11180938	0.82[ASN][1000 genomes]
rs11180941	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11180944	0.89[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11180946	0.82[ASN][1000 genomes]
rs11180947	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs11180948	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs11180949	0.89[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11180950	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11180952	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs11180953	0.85[ASN][1000 genomes]
rs11180954	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11180957	0.85[ASN][1000 genomes]
rs11180959	0.89[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11180962	0.88[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11180963	0.88[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11180964	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11180965	0.89[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11180966	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs11180967	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs11180968	0.89[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11180969	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs11180970	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180971	1.00[EUR][1000 genomes]
rs11180972	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180973	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180974	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180976	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180978	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180982	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180989	1.00[JPT][hapmap]
rs11180995	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180997	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11181000	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11181005	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11181010	0.90[JPT][hapmap]
rs12227303	0.91[JPT][hapmap]
rs12227540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228172	0.89[CHB][hapmap]
rs12230294	0.89[CHB][hapmap]
rs12231433	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12231803	0.89[CHB][hapmap]
rs12232019	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12581707	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12582035	0.85[ASN][1000 genomes]
rs12582204	0.89[CHB][hapmap]
rs12582909	0.91[JPT][hapmap]
rs12582987	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs1379766	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs1458153	1.00[JPT][hapmap]
rs1458172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1458173	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17129417	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs17129436	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17129470	0.90[JPT][hapmap]
rs17835484	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918230	0.89[CHB][hapmap]
rs2125289	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252312	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs285578	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs3214027	0.89[CHB][hapmap]
rs4635145	1.00[EUR][1000 genomes]
rs59955144	1.00[EUR][1000 genomes]
rs6582337	1.00[EUR][1000 genomes]
rs713288	1.00[EUR][1000 genomes]
rs725527	1.00[JPT][hapmap]
rs7968280	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs7969769	0.89[CHB][hapmap]
rs7979435	0.89[CHB][hapmap]
rs9652045	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
2	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain
3	chr12:41904600-41915600	Weak transcription	Fetal Kidney	kidney
4	chr12:41905200-41916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:41907800-41915400	Weak transcription	Fetal Stomach	stomach
6	chr12:41908000-41915400	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:41908000-41915800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:41908200-41915400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:41908600-41915400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:41908800-41915000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:41908800-41915600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:41909600-41915400	Weak transcription	Brain Substantia Nigra	brain
13	chr12:41909800-41915400	Weak transcription	Brain Germinal Matrix	brain
14	chr12:41910200-41915600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:41910400-41915000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:41910600-41915600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:41914000-41915000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:41914000-41917200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:41914400-41915000	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr12:41914600-41915400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:41914600-41915600	Enhancers	HSMMtube	muscle
22	chr12:41914600-41915800	Enhancers	NHLF	lung
23	chr12:41914600-41917400	Enhancers	HSMM	muscle
24	chr12:41914800-41915600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr12:41914800-41915600	Weak transcription	Stomach Smooth Muscle	stomach

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