Variant report

Variant	rs59708508
Chromosome Location	chr16:46918908-46918909
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	chr16:46822185..46825488-chr16:46917726..46919426,3	K562	blood:

Variant related genes	Relation type
ENSG00000140795	Chromatin interaction
ENSG00000260782	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1009391	0.81[EUR][1000 genomes]
rs11860484	0.87[EUR][1000 genomes]
rs11861896	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12935606	0.85[EUR][1000 genomes]
rs1869006	0.89[EUR][1000 genomes]
rs2192644	0.87[EUR][1000 genomes]
rs4246381	0.80[EUR][1000 genomes]
rs4966706	0.89[EUR][1000 genomes]
rs4966708	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4966710	0.88[EUR][1000 genomes]
rs4966713	0.87[EUR][1000 genomes]
rs4967576	0.81[EUR][1000 genomes]
rs4967602	0.90[EUR][1000 genomes]
rs4967621	0.87[EUR][1000 genomes]
rs56006015	0.85[EUR][1000 genomes]
rs56042735	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56354199	0.84[EUR][1000 genomes]
rs57127559	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs58074838	0.82[EUR][1000 genomes]
rs62057633	0.81[EUR][1000 genomes]
rs6598777	0.88[EUR][1000 genomes]
rs67211229	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs67369452	0.87[EUR][1000 genomes]
rs7186748	0.85[EUR][1000 genomes]
rs7192574	0.81[EUR][1000 genomes]
rs7196375	0.84[EUR][1000 genomes]
rs7197485	0.83[EUR][1000 genomes]
rs72812428	0.89[EUR][1000 genomes]
rs8053137	0.84[EUR][1000 genomes]
rs9328668	0.86[EUR][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	esv3326361	chr16:46917676-46920224	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59708508	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46917200-46919000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr16:46917200-46919000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr16:46917200-46919400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:46917200-46919400	Active TSS	Liver	Liver
5	chr16:46917200-46919600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr16:46917200-46919800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr16:46917200-46920800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr16:46917200-46921200	Active TSS	Pancreas	Pancrea
9	chr16:46917400-46919000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr16:46917400-46919000	Active TSS	Aorta	Aorta
11	chr16:46917400-46919000	Active TSS	Colon Smooth Muscle	Colon
12	chr16:46917400-46919000	Active TSS	Osteobl	bone
13	chr16:46917400-46919200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
14	chr16:46917400-46919200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr16:46917400-46919400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr16:46917400-46919400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr16:46917400-46919600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr16:46917400-46919600	Active TSS	Brain Anterior Caudate	brain
19	chr16:46917400-46919600	Active TSS	Right Atrium	heart
20	chr16:46917400-46919800	Active TSS	Brain Angular Gyrus	brain
21	chr16:46917400-46920200	Active TSS	Fetal Kidney	kidney
22	chr16:46917400-46920400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr16:46917400-46920800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:46917600-46919000	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr16:46917600-46919000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:46917600-46919000	Active TSS	Brain Substantia Nigra	brain
27	chr16:46917600-46919000	Active TSS	Small Intestine	intestine
28	chr16:46917600-46919000	Active TSS	A549	lung
29	chr16:46917600-46919200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr16:46917600-46919200	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr16:46917600-46919200	Bivalent/Poised TSS	Thymus	Thymus
32	chr16:46917600-46919400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:46917600-46919400	Active TSS	Stomach Mucosa	stomach
34	chr16:46917600-46919600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr16:46917600-46919600	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr16:46917600-46919600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr16:46917600-46919600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr16:46917600-46919600	Active TSS	Fetal Brain Female	brain
39	chr16:46917600-46919800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr16:46917600-46919800	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr16:46917600-46919800	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr16:46917600-46920000	Active TSS	Esophagus	oesophagus
43	chr16:46917600-46920600	Active TSS	Gastric	stomach
44	chr16:46917800-46919000	Active TSS	H1 Cell Line	embryonic stem cell
45	chr16:46917800-46919000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:46917800-46919000	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr16:46917800-46919000	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr16:46917800-46919000	Active TSS	Fetal Brain Male	brain
49	chr16:46917800-46919000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
50	chr16:46917800-46919000	Active TSS	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links