Variant report

Variant	rs12274021
Chromosome Location	chr11:10162227-10162228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10128609	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10128701	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10840370	0.81[AFR][1000 genomes]
rs11042565	1.00[EUR][1000 genomes]
rs11042584	1.00[EUR][1000 genomes]
rs11042590	0.95[LWK][hapmap]
rs11042616	1.00[EUR][1000 genomes]
rs11042619	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11042631	0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11042651	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11042670	0.96[AFR][1000 genomes]
rs11042672	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042684	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11042691	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042694	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042696	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042697	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042698	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042701	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042705	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042707	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042708	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042709	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042710	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042711	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042715	0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11042722	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12269976	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12270074	1.00[AMR][1000 genomes]
rs12270278	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12270822	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12271159	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12271480	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12272306	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12273035	1.00[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12275641	1.00[EUR][1000 genomes]
rs12276925	1.00[EUR][1000 genomes]
rs12277936	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12279495	1.00[EUR][1000 genomes]
rs12279727	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12279936	0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12280877	1.00[EUR][1000 genomes]
rs12281072	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs12282728	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12285084	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12285093	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12287964	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12288716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12288833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12291188	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12291783	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12292901	1.00[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12294052	1.00[EUR][1000 genomes]
rs12294064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13377400	0.92[AFR][1000 genomes]
rs13377561	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1372812	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16907612	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16907632	1.00[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4537746	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4625455	0.81[YRI][hapmap]
rs5005	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55919524	1.00[EUR][1000 genomes]
rs56948226	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57138875	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57672320	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57743646	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58354844	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59629505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59651099	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59709366	1.00[EUR][1000 genomes]
rs59928017	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60051250	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60433518	1.00[AMR][1000 genomes]
rs7942109	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1039636	chr11:10126747-10280570	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1036041	chr11:10131018-10212202	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv520415	chr11:10159237-10164456	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12274021	SBF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10144800-10170400	Weak transcription	Left Ventricle	heart
2	chr11:10149200-10162800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr11:10156800-10168800	Weak transcription	Fetal Lung	lung
4	chr11:10157000-10177400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:10160800-10162400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:10160800-10162400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:10160800-10162400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:10160800-10162400	Enhancers	Hela-S3	cervix
9	chr11:10160800-10162400	Enhancers	HMEC	breast
10	chr11:10160800-10162400	Enhancers	HUVEC	blood vessel
11	chr11:10160800-10162400	Enhancers	NHEK	skin
12	chr11:10160800-10163000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:10160800-10164600	Enhancers	NHDF-Ad	bronchial
14	chr11:10161200-10162400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr11:10161200-10162400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:10161400-10162400	Enhancers	Right Ventricle	heart
17	chr11:10161400-10162400	Enhancers	HSMM	muscle
18	chr11:10161400-10162400	Enhancers	NHLF	lung
19	chr11:10161400-10163000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:10161600-10162400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:10161800-10162400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:10162000-10162400	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr11:10162000-10162800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:10162000-10166400	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:10162000-10166600	Weak transcription	Ovary	ovary
26	chr11:10162200-10163600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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