Variant report

Variant	rs4966708
Chromosome Location	chr16:46924657-46924658
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46916956..46921483-chr16:46924468..46930263,8	MCF-7	breast:
2	chr16:46923713..46925987-chr16:46943511..46946070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166123	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1009391	0.86[CEU][hapmap];1.00[GIH][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	1.00[GIH][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861896	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934580	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935606	0.94[EUR][1000 genomes]
rs1641122	1.00[ASN][1000 genomes]
rs1651654	1.00[GIH][hapmap]
rs16948661	1.00[GIH][hapmap];0.81[YRI][hapmap]
rs17189741	0.88[GIH][hapmap]
rs1869006	0.86[CEU][hapmap];1.00[GIH][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	1.00[ASN][1000 genomes]
rs35354454	0.84[EUR][1000 genomes]
rs36481	1.00[GIH][hapmap]
rs4246381	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401068	0.88[GIH][hapmap]
rs4966706	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	1.00[GIH][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	1.00[GIH][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.94[EUR][1000 genomes]
rs56042735	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.93[EUR][1000 genomes]
rs57127559	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	1.00[ASN][1000 genomes]
rs58074838	0.90[EUR][1000 genomes]
rs59708508	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62057633	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67211229	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	1.00[ASN][1000 genomes]
rs7186748	0.94[EUR][1000 genomes]
rs7187475	1.00[GIH][hapmap];0.81[YRI][hapmap]
rs7192574	0.89[EUR][1000 genomes]
rs7196375	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197033	1.00[GIH][hapmap];0.81[YRI][hapmap]
rs7197485	0.88[GIH][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812428	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734309	0.87[GIH][hapmap]
rs8044443	1.00[GIH][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs8051017	1.00[GIH][hapmap];0.81[YRI][hapmap]
rs8053137	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	1.00[ASN][1000 genomes]
rs8058734	1.00[ASN][1000 genomes]
rs808432	1.00[ASN][1000 genomes]
rs808783	0.88[GIH][hapmap]
rs9328668	1.00[GIH][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.88[EUR][1000 genomes];1.00[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	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	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription 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	39 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4966708	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46919000-46945400	Weak transcription	Aorta	Aorta
2	chr16:46919000-46963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:46919200-46927600	Weak transcription	Ovary	ovary
4	chr16:46919200-46931600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr16:46919200-46933200	Weak transcription	HUVEC	blood vessel
6	chr16:46919200-46934400	Weak transcription	Lung	lung
7	chr16:46919400-46927800	Weak transcription	Colon Smooth Muscle	Colon
8	chr16:46919400-46931600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:46919600-46929800	Weak transcription	Right Atrium	heart
10	chr16:46919600-46931400	Weak transcription	Spleen	Spleen
11	chr16:46919600-46934200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr16:46919800-46927600	Weak transcription	Right Ventricle	heart
13	chr16:46920000-46931800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:46920200-46927600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr16:46920200-46944800	Weak transcription	Hela-S3	cervix
16	chr16:46920400-46928000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr16:46920400-46928000	Weak transcription	HSMMtube	muscle
18	chr16:46920400-46928800	Weak transcription	Osteobl	bone
19	chr16:46920600-46929600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr16:46920600-46933000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:46920800-46925400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:46920800-46927600	Weak transcription	Placenta	Placenta
23	chr16:46920800-46928000	Weak transcription	Fetal Kidney	kidney
24	chr16:46920800-46929000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:46920800-46929400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:46920800-46936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr16:46920800-46940600	Weak transcription	HMEC	breast
28	chr16:46920800-46949000	Weak transcription	A549	lung
29	chr16:46921000-46927800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr16:46921000-46928000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr16:46921000-46928000	Weak transcription	NH-A	brain
32	chr16:46921000-46928400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:46921000-46944400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr16:46921200-46927600	Weak transcription	Fetal Brain Male	brain
35	chr16:46921400-46924800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr16:46921600-46926000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr16:46921800-46926800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr16:46921800-46929400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr16:46921800-46941600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr16:46922000-46927600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:46922000-46927800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr16:46922200-46927600	Weak transcription	Fetal Lung	lung
43	chr16:46922200-46928000	Weak transcription	HSMM	muscle
44	chr16:46922200-46928400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr16:46922200-46929800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:46922400-46927800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr16:46922600-46926600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr16:46923000-46924800	Enhancers	Adipose Nuclei	Adipose
49	chr16:46923200-46925200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr16:46923600-46929600	Weak transcription	H9 Cell Line	embryonic stem cell

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