Variant report

Variant	rs12935606
Chromosome Location	chr16:46968249-46968250
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1009391	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs11860484	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11861896	0.94[EUR][1000 genomes]
rs12931259	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12934580	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1869006	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs2192644	0.91[EUR][1000 genomes]
rs35354454	0.81[EUR][1000 genomes]
rs4246381	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs4966706	0.90[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4966708	0.94[EUR][1000 genomes]
rs4966710	0.97[EUR][1000 genomes]
rs4966713	0.90[CEU][hapmap];0.99[EUR][1000 genomes]
rs4967576	0.85[EUR][1000 genomes]
rs4967602	0.81[CEU][hapmap];0.95[EUR][1000 genomes]
rs4967621	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56006015	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56042735	0.95[EUR][1000 genomes]
rs56354199	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57127559	0.90[EUR][1000 genomes]
rs58074838	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59708508	0.85[EUR][1000 genomes]
rs62057633	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6598777	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67211229	0.90[EUR][1000 genomes]
rs67369452	0.99[EUR][1000 genomes]
rs7186748	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7192574	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7196375	0.89[EUR][1000 genomes]
rs7197485	0.87[EUR][1000 genomes]
rs72812428	0.94[EUR][1000 genomes]
rs734309	0.90[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs8053137	0.88[EUR][1000 genomes]
rs9328668	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs9889198	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	esv1799095	chr16:46916670-46972671	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1063660	chr16:46930623-46978792	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12935606	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46930800-46968400	Weak transcription	Right Atrium	heart
2	chr16:46961800-46988600	Weak transcription	Hela-S3	cervix
3	chr16:46963400-46969200	Weak transcription	Aorta	Aorta
4	chr16:46964000-46970800	Weak transcription	K562	blood
5	chr16:46964200-46976800	Weak transcription	Placenta	Placenta
6	chr16:46964200-46990600	Weak transcription	Spleen	Spleen
7	chr16:46964200-46991800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr16:46964600-46970200	Weak transcription	Gastric	stomach
9	chr16:46964600-46988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:46964800-46988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr16:46965000-46990600	Weak transcription	Esophagus	oesophagus
12	chr16:46965200-46970000	Weak transcription	Fetal Muscle Leg	muscle
13	chr16:46965200-46973600	Weak transcription	Pancreas	Pancrea
14	chr16:46965200-46977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr16:46965200-46977400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr16:46965200-46988000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr16:46965200-46990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr16:46965400-46977200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr16:46965400-46988000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:46965400-46988600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr16:46965400-46988600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:46965800-46969800	Weak transcription	Brain Germinal Matrix	brain
23	chr16:46966000-46988800	Weak transcription	Fetal Brain Female	brain
24	chr16:46967000-46977200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:46967200-46972400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr16:46967400-46969400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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