Variant report

Variant	rs734309
Chromosome Location	chr16:46952031-46952032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46951055..46952888-chr16:46955972..46959090,3	K562	blood:
2	chr16:46933814..46935655-chr16:46950387..46952278,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166123	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1009391	0.89[GIH][hapmap]
rs11860484	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs12931259	0.87[AFR][1000 genomes]
rs12934580	0.87[AMR][1000 genomes]
rs12935606	0.85[AMR][1000 genomes]
rs1651654	0.89[GIH][hapmap]
rs16948661	0.89[GIH][hapmap]
rs1869006	0.89[GIH][hapmap]
rs36481	0.89[GIH][hapmap]
rs4966708	0.87[GIH][hapmap]
rs4966713	0.89[GIH][hapmap]
rs4967602	0.89[GIH][hapmap]
rs4967621	0.83[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];0.87[AMR][1000 genomes]
rs6598777	0.84[AMR][1000 genomes]
rs7186748	0.85[AMR][1000 genomes]
rs7187475	0.89[GIH][hapmap]
rs7197033	0.89[GIH][hapmap]
rs7197485	0.83[ASW][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs8044443	0.89[GIH][hapmap]
rs8051017	0.89[GIH][hapmap]
rs9328668	0.89[GIH][hapmap]

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	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	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1831215	chr16:46907546-46962858	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	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
11	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
rs734309	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46919000-46963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:46928400-46966000	Strong transcription	Fetal Brain Female	brain
3	chr16:46929400-46965200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:46930600-46956200	Weak transcription	Fetal Intestine Small	intestine
5	chr16:46930800-46965400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr16:46930800-46968400	Weak transcription	Right Atrium	heart
7	chr16:46931200-46952400	Weak transcription	Ovary	ovary
8	chr16:46931600-46957800	Strong transcription	Fetal Stomach	stomach
9	chr16:46931600-46965200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr16:46932200-46956200	Weak transcription	Left Ventricle	heart
11	chr16:46932200-46965200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:46932400-46957600	Weak transcription	Psoas Muscle	Psoas
13	chr16:46933600-46959800	Weak transcription	HUVEC	blood vessel
14	chr16:46933600-46965400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr16:46933800-46965800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr16:46934000-46963400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr16:46935400-46958200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr16:46936600-46956000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr16:46936600-46956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr16:46938600-46952600	Weak transcription	Stomach Mucosa	stomach
21	chr16:46939600-46964800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:46940000-46964600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr16:46941200-46955000	Enhancers	Primary B cells from peripheral blood	blood
24	chr16:46942800-46956200	Weak transcription	Colon Smooth Muscle	Colon
25	chr16:46943000-46952200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr16:46943000-46952400	Strong transcription	Placenta	Placenta
27	chr16:46943000-46952400	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr16:46943200-46965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:46943200-46965400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr16:46943400-46953400	Strong transcription	HSMMtube	muscle
31	chr16:46943400-46953600	Strong transcription	Adipose Nuclei	Adipose
32	chr16:46943400-46954800	Strong transcription	Fetal Muscle Leg	muscle
33	chr16:46943400-46965000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr16:46943400-46965000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr16:46943400-46965200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr16:46943400-46965400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:46943400-46965400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:46943400-46965400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr16:46943600-46959400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:46943800-46953000	Weak transcription	Colonic Mucosa	Colon
41	chr16:46944400-46952200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr16:46945200-46957400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr16:46945400-46955000	Strong transcription	Brain Germinal Matrix	brain
44	chr16:46945600-46953000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr16:46945600-46954200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr16:46945800-46965200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr16:46945800-46965400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr16:46946000-46955200	Weak transcription	Hela-S3	cervix
49	chr16:46946200-46957800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:46946400-46953400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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