Variant report

Variant	rs6598777
Chromosome Location	chr16:46933997-46933998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:46892340..46895420-chr16:46933101..46936147,3	MCF-7	breast:
2	chr16:46932297..46935211-chr16:46938670..46940478,2	K562	blood:
3	chr16:46933814..46935655-chr16:46950387..46952278,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1009391	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861896	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12931259	0.81[EUR][1000 genomes]
rs12934580	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935606	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1641122	1.00[ASN][1000 genomes]
rs1869006	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	1.00[ASN][1000 genomes]
rs35354454	0.83[EUR][1000 genomes]
rs4246381	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966706	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966708	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56042735	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57127559	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57942848	1.00[ASN][1000 genomes]
rs58074838	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59708508	0.88[EUR][1000 genomes]
rs62057633	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67211229	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	1.00[ASN][1000 genomes]
rs7186748	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7192574	0.93[EUR][1000 genomes]
rs7196375	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197485	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812428	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734309	0.84[AMR][1000 genomes]
rs8044443	1.00[ASN][1000 genomes]
rs8053137	0.91[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]
rs9328668	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	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
rs6598777	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 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	chr16:46919200-46934400	Weak transcription	Lung	lung
4	chr16:46919600-46934200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr16:46920200-46944800	Weak transcription	Hela-S3	cervix
6	chr16:46920800-46936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:46920800-46940600	Weak transcription	HMEC	breast
8	chr16:46920800-46949000	Weak transcription	A549	lung
9	chr16:46921000-46944400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr16:46921800-46941600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr16:46924200-46941200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr16:46927400-46936600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:46928400-46942400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr16:46928400-46966000	Strong transcription	Fetal Brain Female	brain
15	chr16:46928600-46937200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:46929000-46949200	Weak transcription	Fetal Brain Male	brain
17	chr16:46929200-46949200	Weak transcription	K562	blood
18	chr16:46929400-46965200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr16:46929600-46934400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr16:46929800-46941200	Strong transcription	Brain Germinal Matrix	brain
21	chr16:46930200-46937800	Weak transcription	Colonic Mucosa	Colon
22	chr16:46930200-46940800	Weak transcription	Fetal Intestine Large	intestine
23	chr16:46930400-46934400	Genic enhancers	Gastric	stomach
24	chr16:46930400-46938200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr16:46930600-46934200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr16:46930600-46956200	Weak transcription	Fetal Intestine Small	intestine
27	chr16:46930800-46934800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr16:46930800-46934800	Genic enhancers	HepG2	liver
29	chr16:46930800-46935800	Weak transcription	Brain Substantia Nigra	brain
30	chr16:46930800-46941800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:46930800-46965400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:46930800-46968400	Weak transcription	Right Atrium	heart
33	chr16:46931000-46939800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr16:46931000-46946800	Weak transcription	Fetal Lung	lung
35	chr16:46931000-46949000	Weak transcription	Fetal Kidney	kidney
36	chr16:46931000-46951200	Strong transcription	Liver	Liver
37	chr16:46931200-46941600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr16:46931200-46942200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr16:46931200-46952400	Weak transcription	Ovary	ovary
40	chr16:46931400-46940800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr16:46931400-46941400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr16:46931600-46934800	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr16:46931600-46936200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr16:46931600-46936400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr16:46931600-46936600	Genic enhancers	Esophagus	oesophagus
46	chr16:46931600-46938000	Strong transcription	Brain Hippocampus Middle	brain
47	chr16:46931600-46941000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr16:46931600-46957800	Strong transcription	Fetal Stomach	stomach
49	chr16:46931600-46965200	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr16:46931800-46934600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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