Variant report

Variant	rs12934839
Chromosome Location	chr16:81169993-81169994
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:81169984-81170233	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81128511..81130849-chr16:81169835..81172966,4	MCF-7	breast:
2	chr16:81110384..81110935-chr16:81169785..81170782,2	MCF-7	breast:
3	chr16:71843029..71844532-chr16:81169189..81171698,2	MCF-7	breast:
4	chr16:81167266..81170181-chr16:81212814..81215037,2	MCF-7	breast:

Variant related genes	Relation type
PKD1L2	TF binding region
ENSG00000140905	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000166473	Chromatin interaction
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11150347	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12597420	0.83[ASN][1000 genomes]
rs12918619	0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12920229	0.85[JPT][hapmap]
rs34748822	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889243	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv530715	chr16:81117168-81252875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv907005	chr16:81121353-81194912	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1067144	chr16:81129298-81181641	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1056843	chr16:81154448-81172662	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv907007	chr16:81157521-81181423	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv978328	chr16:81166830-81197232	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81130000-81187600	Weak transcription	Right Atrium	heart
2	chr16:81151400-81173000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:81154000-81198800	Weak transcription	Right Ventricle	heart
4	chr16:81155400-81174600	Weak transcription	Left Ventricle	heart
5	chr16:81163800-81170600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:81165800-81174800	Weak transcription	Spleen	Spleen
7	chr16:81167200-81181000	Enhancers	Placenta	Placenta
8	chr16:81168800-81174000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr16:81169600-81170000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:81169600-81170200	Enhancers	Brain Angular Gyrus	brain
11	chr16:81169600-81170200	Enhancers	Brain Anterior Caudate	brain
12	chr16:81169600-81170400	Enhancers	Brain Hippocampus Middle	brain
13	chr16:81169600-81170400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr16:81169600-81170600	Enhancers	Brain Cingulate Gyrus	brain
15	chr16:81169600-81171200	Enhancers	Fetal Brain Female	brain
16	chr16:81169600-81171600	Enhancers	Brain Germinal Matrix	brain
17	chr16:81169600-81171600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr16:81169600-81171800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr16:81169600-81171800	Enhancers	Fetal Brain Male	brain
20	chr16:81169600-81173400	Enhancers	Adipose Nuclei	Adipose
21	chr16:81169800-81170000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:81169800-81170000	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr16:81169800-81170000	Enhancers	Esophagus	oesophagus
24	chr16:81169800-81170200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:81169800-81170200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr16:81169800-81170200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr16:81169800-81170200	Enhancers	NHDF-Ad	bronchial
28	chr16:81169800-81170400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr16:81169800-81170600	Enhancers	HepG2	liver
30	chr16:81169800-81170800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr16:81169800-81171000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr16:81169800-81171000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr16:81169800-81171200	Enhancers	Fetal Muscle Leg	muscle
34	chr16:81169800-81171200	Enhancers	Ovary	ovary
35	chr16:81169800-81171400	Enhancers	Fetal Lung	lung
36	chr16:81169800-81171400	Enhancers	A549	lung
37	chr16:81169800-81171600	Enhancers	Fetal Stomach	stomach

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