Variant report

Variant	rs12192605
Chromosome Location	chr6:133421492-133421493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10457002	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10457600	0.87[EUR][1000 genomes]
rs10457602	1.00[CEU][hapmap]
rs10457603	1.00[CEU][hapmap]
rs11154715	0.84[EUR][1000 genomes]
rs12154207	0.84[EUR][1000 genomes]
rs12190728	0.84[EUR][1000 genomes]
rs12191026	0.84[EUR][1000 genomes]
rs12192002	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193118	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12196069	0.83[EUR][1000 genomes]
rs12196492	0.84[EUR][1000 genomes]
rs12198619	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12199138	0.87[EUR][1000 genomes]
rs12199555	0.84[EUR][1000 genomes]
rs12199958	0.84[EUR][1000 genomes]
rs12199972	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12200393	0.84[EUR][1000 genomes]
rs12201315	1.00[CEU][hapmap]
rs12205139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12206291	0.82[EUR][1000 genomes]
rs12210093	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12210216	0.84[EUR][1000 genomes]
rs12211999	0.84[EUR][1000 genomes]
rs12212715	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12213350	0.87[EUR][1000 genomes]
rs12213452	0.87[EUR][1000 genomes]
rs12213690	0.84[EUR][1000 genomes]
rs12215217	0.87[EUR][1000 genomes]
rs17062051	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs28538690	0.94[EUR][1000 genomes]
rs4077767	0.91[EUR][1000 genomes]
rs4077768	0.87[EUR][1000 genomes]
rs4257872	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4273707	0.96[EUR][1000 genomes]
rs4273708	0.96[EUR][1000 genomes]
rs4895949	0.81[EUR][1000 genomes]
rs4895952	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57161827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58835706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59793266	0.84[EUR][1000 genomes]
rs62428563	0.86[EUR][1000 genomes]
rs62428596	0.84[EUR][1000 genomes]
rs62428597	0.83[EUR][1000 genomes]
rs62430562	0.91[EUR][1000 genomes]
rs62430580	0.89[EUR][1000 genomes]
rs62430581	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62430582	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62430588	0.96[EUR][1000 genomes]
rs62430590	0.96[EUR][1000 genomes]
rs6569863	0.81[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap]
rs6902225	0.87[EUR][1000 genomes]
rs6902347	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6911954	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6913444	0.83[EUR][1000 genomes]
rs6915521	0.81[EUR][1000 genomes]
rs6927627	0.96[EUR][1000 genomes]
rs6933214	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6935070	0.96[EUR][1000 genomes]
rs6935480	0.96[EUR][1000 genomes]
rs6935677	0.81[EUR][1000 genomes]
rs6936410	0.96[EUR][1000 genomes]
rs6937029	0.95[EUR][1000 genomes]
rs6939899	0.91[EUR][1000 genomes]
rs6940959	0.96[EUR][1000 genomes]
rs72557636	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738156	0.96[EUR][1000 genomes]
rs7738592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7745056	0.81[EUR][1000 genomes]
rs7746390	0.84[EUR][1000 genomes]
rs7748926	0.83[EUR][1000 genomes]
rs7750218	0.84[EUR][1000 genomes]
rs7750279	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7750376	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7754486	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7756171	0.95[CEU][hapmap];0.92[CHB][hapmap];0.91[EUR][1000 genomes]
rs7756963	0.84[EUR][1000 genomes]
rs7761372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767651	0.84[EUR][1000 genomes]
rs7770031	0.84[EUR][1000 genomes]
rs9321388	0.91[EUR][1000 genomes]
rs9321389	0.91[EUR][1000 genomes]
rs9483529	0.96[EUR][1000 genomes]
rs9483530	0.96[EUR][1000 genomes]
rs9483535	0.91[EUR][1000 genomes]
rs9483554	0.81[EUR][1000 genomes]
rs9493513	0.93[EUR][1000 genomes]
rs9493514	0.87[EUR][1000 genomes]
rs9493515	0.96[EUR][1000 genomes]
rs9493517	0.96[EUR][1000 genomes]
rs9493518	0.96[EUR][1000 genomes]
rs957183	0.84[EUR][1000 genomes]
rs975225	0.92[CHB][hapmap];0.92[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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv428154	chr6:133271975-133522803	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3445931	chr6:133347824-133434532	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv519475	chr6:133350936-133474673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12192605	HBS1L	cis	parietal	SCAN
rs12192605	VNN2	cis	cerebellum	SCAN
rs12192605	HBS1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133417200-133422200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:133417200-133422600	Weak transcription	Brain Substantia Nigra	brain
3	chr6:133418800-133422800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:133419400-133422800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:133419400-133422800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:133420000-133423200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:133420200-133421600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:133420200-133421800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:133421000-133422200	Weak transcription	Brain Anterior Caudate	brain
10	chr6:133421000-133422200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:133421000-133422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:133421200-133429200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:133421400-133421800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:133421400-133422600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:133421400-133422600	Weak transcription	NH-A	brain
16	chr6:133421400-133422600	Weak transcription	NHLF	lung
17	chr6:133421400-133423000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:133421400-133423200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:133421400-133425400	Weak transcription	Hela-S3	cervix

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