Variant report

Variant	rs16923129
Chromosome Location	chr12:20849727-20849728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLCO1C1-1	chr12:20849683-20849909	NONHSAT027231

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12809210	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12809378	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12811837	0.94[EUR][1000 genomes]
rs12819256	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12820620	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12831009	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1515779	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16915410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34000404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34167698	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34425791	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35018358	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35123559	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67481714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71446707	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71446708	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71446709	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71446712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71446713	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71446714	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71446715	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7306841	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7960372	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv557704	chr12:20842041-20893980	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20838800-20849800	Weak transcription	Hela-S3	cervix
2	chr12:20847800-20849800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr12:20847800-20850000	Active TSS	Brain Anterior Caudate	brain
4	chr12:20848000-20849800	Active TSS	Brain Hippocampus Middle	brain
5	chr12:20848400-20849800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:20848400-20849800	Enhancers	Fetal Muscle Leg	muscle
7	chr12:20848400-20851800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:20848600-20851600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:20848600-20852000	Active TSS	Fetal Brain Female	brain
10	chr12:20848800-20849800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:20848800-20851400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:20849000-20849800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:20849400-20849800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:20849400-20849800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:20849400-20849800	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr12:20849400-20849800	Enhancers	Fetal Lung	lung
17	chr12:20849400-20850200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr12:20849400-20850800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:20849400-20851800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:20849600-20849800	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr12:20849600-20850000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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